Required Packages

library(missMethyl)
library(IlluminaHumanMethylationEPICanno.ilm10b4.hg19)
library(kableExtra)
library(IlluminaHumanMethylation450kanno.ilmn12.hg19)
library(dplyr)

ann850k = getAnnotation(IlluminaHumanMethylationEPICanno.ilm10b4.hg19)
ann450k = getAnnotation(IlluminaHumanMethylation450kanno.ilmn12.hg19)

ann450kUnique = ann450k[!(rownames(ann450k) %in% rownames(ann850k)),]
dim(ann450kUnique)
# 33059    33

annAll = rbind(ann850k[,c('Name', 'chr', 'pos', "UCSC_RefGene_Name", "UCSC_RefGene_Group")], ann450kUnique[,c('Name', 'chr', 'pos', "UCSC_RefGene_Name", "UCSC_RefGene_Group")])
annAll = data.frame(annAll)

setwd('/Users/annebozack/Documents/arsenic_meta/generic-metal')

Functions

metalProcess = function(table, anno){
    colnames(table) = table[1,]
    colnames(table)[1] = 'Name'
    table = table[-1,]
    table = table[,-c(2,3)]
    table[,2] = as.numeric(table[,2])
    table[,3] = as.numeric(table[,3])
    table[,4] = as.numeric(table[,4])

    table$P.FDR = p.adjust(table[,4], method='fdr')
    table$P.Bonf = p.adjust(table[,4], method='bonferroni')
    
    table = merge(table, annAll, by = 'Name', all.y = F)
    table = data.frame(table)
    
    table = table[order(table[,4]),]

    return(table)
}

manhattan_meta = function(probe, colors = c("#2D728F", "#2B4162"), FDR = FALSE){
    probe$chr = as.numeric(gsub("chr", "", probe$chr))

    don = probe %>% 
        # Compute chromosome size
            group_by(chr) %>% summarise(chr_len=as.numeric(max(pos))) %>% 
        # Calculate cumulative position of each chromosome
            mutate(tot=cumsum(chr_len)-chr_len) %>% dplyr::select(-chr_len) %>%
        # Add this info to the initial dataset
            left_join(probe, ., by=c("chr"="chr")) %>%
        # Add a cumulative position of each site
            arrange(chr, pos) %>% mutate(poscum=pos+tot) # %>%
        # Add highlight and annotation information
            # mutate(is_highlight=ifelse(SNP %in% snpsOfInterest, "yes", "no")) %>%
            # mutate(is_annotate_fdr=ifelse(adj.P.Val<0.05 & adj.P.Val.bonf>0.05, "yes", "no")) %>%
            # mutate(is_annotate_bonf=ifelse(adj.P.Val.bonf <0.05, "yes", "no"))
            # don$alpha[don$is_annotate_fdr == 'no'] = 0.6
            # don$alpha[don$is_annotate_fdr == 'yes'] = 0
        # Prepare X axis
            axisdf = don %>% group_by(chr) %>% summarize(center=(max(poscum) + min(poscum))/2)
    don = merge(don, probe[,c(1,11)], on='cpg', all.x=T)
    
    if (FDR){
        FRDalpha = 0.5
    } else {
        FRDalpha = 0
    }

    manhattan = ggplot(don, aes(x=poscum, y=-log10(P.value))) +
    geom_point(aes(color=as.factor(chr)), size=0.8, alpha = 0.55) + scale_color_manual(values = rep(colors, dim(table(don$chr)))) +
    # p-value cutoffs
    geom_hline(yintercept=-log10(0.05/nrow(don)), colour = '#AB3428', size=.3, alpha = 0.5) +
    geom_hline(yintercept=-log10(max(don$P.value[don$P.FDR < 0.05])), colour='#AB3428', size=.3, alpha = FRDalpha, linetype = "dashed") +
    # custom axes:
    scale_x_continuous(expand = c(0.005, 0.005), limits = c(min(don$poscum), max(don$poscum)), label = axisdf$chr, breaks= axisdf$center) +
    scale_y_continuous(expand = c(0, 0), limits = c(0, (max(-log10(don$P.value)) + 0.5)), breaks = seq(from = 0, to = (max(-log10(don$P.value)) + 0.5), by = 1)) + 
    # Custom theme:
    theme_minimal() + theme( 
    legend.position="none", panel.border = element_blank(), panel.grid.minor.y = element_blank(), panel.grid.major.x = element_blank(), panel.grid.minor.x = element_blank(), panel.grid.major.y = element_line(size = 0.2, color = 'gray65')) + theme(text = element_text(size = 7.5)) + 
    labs(y=expression(-log[10]*"(P-value)"), x='Chromosome') 
    
    return(manhattan)
}

lambda <- function(p) median(qchisq(p, df=1, lower.tail=FALSE), na.rm=TRUE) / qchisq(0.5, df=1)

gg_qqplot = function(pvector) {
    l = round(lambda(pvector), 3)
    o = -log10(sort(pvector, decreasing = FALSE))
    e = -log10(ppoints(length(pvector)))
    df = data.frame(o = o, e = e)
    ggplot(df, aes(e, o)) + geom_point(alpha = 0.5, size = 1) + geom_abline(intercept = 0, slope = 1, color = '#AB3428') + labs(y = expression(Observed ~ ~-log[10](italic(p))), x = expression(Expected ~ ~-log[10](italic(p)))) + theme_classic() + annotate("text", x = 1, y = 5, label = paste0('λ = ', l))
}


volcano_meta = function(probe, FDR = FALSE) {
        if (FDR){
            FDRalpha = 0.5
        } else {
            FDRalpha = 0
        }
        
        volcano = ggplot(probe, aes(x= Effect, y = -log10(P.value))) + 
        geom_point(size = 0.8, alpha=0.4) + 
        geom_hline(aes(yintercept = -log10(0.05/nrow(probe)), color = "#AB3428", alpha = 0.5)) + 
        geom_hline(aes(yintercept = -log10(max(P.value[P.FDR < 0.05]))), color = "#AB3428", alpha = FDRalpha, linetype = "dashed") + theme_minimal() + 
        labs(y=expression(-log[10]*"(P-value)"), x='Effect estimate') + theme(panel.grid.minor.y = element_blank()) + theme(text = element_text(size=8)) + 
        scale_y_continuous(expand = c(0, 0), limits = c(0, (max(-log10(probe$P.value)) + 0.5)), breaks = seq(from = 0, to = (max(-log10(probe$P.value)) + 0.5), by = 1)) +
        theme(legend.position="none") + theme(panel.grid.minor.x = element_blank(), panel.grid.major.y = element_line(size = 0.2, color = 'gray65'), panel.grid.major.x = element_line(size = 0.2, color = 'gray65'))
        
        return(volcano)
}

DMPs

DMP datasets for common CpGs

# results adjusted for age, sex, smoking

fact850 = read.table('/Users/annebozack/Documents/arsenic_meta/generic-metal/FACT_DMP_AsCategorical_adjAgeSm_850k_092520.txt', sep = "\t", header = T)
fact450 = read.table('/Users/annebozack/Documents/arsenic_meta/generic-metal/FACT_DMP_AsCategorical_adjAgeSm_450k_092520.txt', sep = "\t", header = T)
chilePBMC = read.table('/Users/annebozack/Documents/arsenic_meta/Chile_PBMCs_DMPs_updated-results_2020-11-29/age-sex-smoking.txt', sep = "\t", header = T)
chileBuccal = read.table('/Users/annebozack/Documents/arsenic_meta/Chile_buccal_DMPs_updated-results_2020-11-29/age-sex-smoking.txt', sep = "\t", header = T)

allCpg = Reduce(intersect, list(fact850$cpg, fact450$cpg, chilePBMC$cpg, chileBuccal$cpg))

fact850 = fact850[fact850$cpg %in% allCpg,]
fact450 = fact450[fact450$cpg %in% allCpg,]
chilePBMC = chilePBMC[chilePBMC$cpg %in% allCpg,]
chileBuccal = chileBuccal[chileBuccal$cpg %in% allCpg,]

write.table(fact850, file = "/Users/annebozack/Documents/arsenic_meta/generic-metal/FACT_DMP_AsCategorical_adjAgeSm_850k_120420_common.txt", sep = "\t", row.names = FALSE, col.names = TRUE)
write.table(fact450, file = "/Users/annebozack/Documents/arsenic_meta/generic-metal/FACT_DMP_AsCategorical_adjAgeSm_450k_120420_common.txt", sep = "\t", row.names = FALSE, col.names = TRUE)
write.table(chilePBMC, file = "/Users/annebozack/Documents/arsenic_meta/generic-metal/chile-pbmcs-age-sex-smoking_120420_common.txt", sep = "\t", row.names = FALSE, col.names = TRUE)
write.table(chileBuccal, file = "/Users/annebozack/Documents/arsenic_meta/generic-metal/chile-buccal-age-sex-smoking_120420_common.txt", sep = "\t", row.names = FALSE, col.names = TRUE)


# results adjusted for age, sex, smoking, cells

fact850cell = read.table('/Users/annebozack/Documents/arsenic_meta/generic-metal/FACT_DMP_AsCategorical_adjCellAgeSm_850k_092520.txt', sep = "\t", header = T)
fact450cell = read.table('/Users/annebozack/Documents/arsenic_meta/generic-metal/FACT_DMP_AsCategorical_adjCellAgeSm_450k_092520.txt', sep = "\t", header = T)
chilePBMCcell = read.table('/Users/annebozack/Documents/arsenic_meta/Chile_PBMCs_DMPs_updated-results_2020-11-29/cell-age-sex-smoking.txt', sep = "\t", header = T)
chileBuccalcell = read.table('/Users/annebozack/Documents/arsenic_meta/Chile_buccal_DMPs_updated-results_2020-11-29/cell-age-sex-smoking.txt', sep = "\t", header = T)

fact850cell = fact850cell[fact850cell$cpg %in% allCpg,]
fact450cell = fact450cell[fact450cell$cpg %in% allCpg,]
chilePBMCcell = chilePBMCcell[chilePBMCcell $cpg %in% allCpg,]
chileBuccalcell = chileBuccalcell[chileBuccalcell$cpg %in% allCpg,]

write.table(fact850cell, file = "/Users/annebozack/Documents/arsenic_meta/generic-metal/FACT_DMP_AsCategorical_adjCellAgeSm_850k_120420_common.txt", sep = "\t", row.names = FALSE, col.names = TRUE)
write.table(fact450cell, file = "/Users/annebozack/Documents/arsenic_meta/generic-metal/FACT_DMP_AsCategorical_adjCellAgeSm_450k_120420_common.txt", sep = "\t", row.names = FALSE, col.names = TRUE)
write.table(chilePBMCcell, file = "/Users/annebozack/Documents/arsenic_meta/generic-metal/chile-pbmcs-cell-age-sex-smoking_120420_common.txt", sep = "\t", row.names = FALSE, col.names = TRUE)
write.table(chileBuccalcell, file = "/Users/annebozack/Documents/arsenic_meta/generic-metal/chile-buccal-cell-age-sex-smoking_120420_common.txt", sep = "\t", row.names = FALSE, col.names = TRUE)

Run in METAL

cd /Users/annebozack/Documents/arsenic_meta/generic-metal

MARKER "cpg"
EFFECT "logFC"
PVAL "P.exitValue"
STDERR "std_err"
SCHEME STDERR

# SCHEME STDERR command and weights effect size estimates using the inverse of the corresponding standard errors
    
# no cell type adjustment, blood only
PROCESS /Users/annebozack/Documents/arsenic_meta/generic-metal/FACT_DMP_AsCategorical_adjAgeSm_850k_120420_common.txt
PROCESS /Users/annebozack/Documents/arsenic_meta/generic-metal/FACT_DMP_AsCategorical_adjAgeSm_450k_120420_common.txt
PROCESS /Users/annebozack/Documents/arsenic_meta/generic-metal/chile-pbmcs-age-sex-smoking_120420_common.txt
OUTFILE /Users/annebozack/Documents/arsenic_meta/generic-metal/blood_no_cell_common_032921 .tbl

ANALYZE HETEROGENEITY

# no cell type adjustment, all samples
PROCESS /Users/annebozack/Documents/arsenic_meta/generic-metal/FACT_DMP_AsCategorical_adjAgeSm_850k_120420_common.txt
PROCESS /Users/annebozack/Documents/arsenic_meta/generic-metal/FACT_DMP_AsCategorical_adjAgeSm_450k_120420_common.txt
PROCESS /Users/annebozack/Documents/arsenic_meta/generic-metal/chile-pbmcs-age-sex-smoking_120420_common.txt
PROCESS /Users/annebozack/Documents/arsenic_meta/generic-metal/chile-buccal-age-sex-smoking_120420_common.txt
OUTFILE /Users/annebozack/Documents/arsenic_meta/generic-metal/all_no_cell_common_120420 .tbl

ANALYZE

# cell type adjustment, blood only  
PROCESS /Users/annebozack/Documents/arsenic_meta/generic-metal/FACT_DMP_AsCategorical_adjCellAgeSm_850k_120420_common.txt
PROCESS /Users/annebozack/Documents/arsenic_meta/generic-metal/FACT_DMP_AsCategorical_adjCellAgeSm_450k_120420_common.txt
PROCESS /Users/annebozack/Documents/arsenic_meta/generic-metal/chile-pbmcs-cell-age-sex-smoking_120420_common.txt
OUTFILE /Users/annebozack/Documents/arsenic_meta/generic-metal/blood_cell_common_120420 .tbl

ANALYZE

# cell type adjustment, all samples
PROCESS /Users/annebozack/Documents/arsenic_meta/generic-metal/FACT_DMP_AsCategorical_adjCellAgeSm_850k_120420_common.txt
PROCESS /Users/annebozack/Documents/arsenic_meta/generic-metal/FACT_DMP_AsCategorical_adjCellAgeSm_450k_120420_common.txt
PROCESS /Users/annebozack/Documents/arsenic_meta/generic-metal/chile-pbmcs-cell-age-sex-smoking_120420_common.txt
PROCESS /Users/annebozack/Documents/arsenic_meta/generic-metal/chile-buccal-cell-age-sex-smoking_120420_common.txt
OUTFILE /Users/annebozack/Documents/arsenic_meta/generic-metal/all_cell_common_120420 .tbl

ANALYZE

Without cell type adjustment

Blood only

metal_blood_noCell = read.table('/Users/annebozack/Documents/arsenic_meta/generic-metal/blood_no_cell_common_1204201.tbl', sep = "\t")

metal_blood_noCell = metalProcess(metal_blood_noCell)

write.csv(metal_blood_noCell, '/Users/annebozack/Documents/arsenic_meta/generic-metal/DMP_blood_no_cell_common_120420.csv')


# Significant probes

# Nominal P-value
table(metal_blood_noCell$P.value < 0.05)
#  FALSE   TRUE 
# 357719  19632 

# FDR
table(metal_blood_noCell$P.FDR < 0.05)
# FALSE 
# 377351 

table(metal_blood_noCell$P.FDR < 0.1)
# FALSE 
# 377351 

# Bonferroni
table(metal_blood_noCell$P.Bonf < 0.05)
# FALSE 
# 377351 


# GO analysis, FDR < 0.1 probes

# NA


# Plotting

gg_qqplot(metal_blood_noCell$P.value)
quartz.save('qq_metal_blood_noCell_120420.png', type = "png", dpi = 300)

manhattan_meta(metal_blood_noCell)
quartz.save('manhattan_metal_blood_noCell_120420.png', type = "png", dpi = 300)

volcano_meta(metal_blood_noCell)
quartz.save('volcano_metal_blood_noCell_120420.png', type = "png", dpi = 300)
knitr::include_graphics("/Users/annebozack/Documents/arsenic_meta/generic-metal/qq_metal_blood_noCell_120420.png")

knitr::include_graphics("/Users/annebozack/Documents/arsenic_meta/generic-metal/manhattan_metal_blood_noCell_120420.png")

knitr::include_graphics("/Users/annebozack/Documents/arsenic_meta/generic-metal/volcano_metal_blood_noCell_120420.png")

Top 100 probes

X Name Effect StdErr P.value Direction P.FDR P.Bonf chr pos UCSC_RefGene_Name UCSC_RefGene_Group
93 cg00004257 0.2473 0.0503 0.0000009 +++ 0.1315697 0.3325217 chr1 34629175 CSMD2 Body
316516 cg22938488 0.1765 0.0365 0.0000013 -++ 0.1315697 0.5045183 chr5 1501670 LPCAT1 Body
114376 cg07490485 0.1711 0.0356 0.0000016 +++ 0.1315697 0.5924411 chr14 50432614
194923 cg13490635 0.2572 0.0537 0.0000016 +++ 0.1315697 0.6207424 chr8 30242021 RBPMS;RBPMS;RBPMS;RBPMS;RBPMS;RBPMS;RBPMS;RBPMS 5’UTR;5’UTR;1stExon;1stExon;1stExon;5’UTR;1stExon;5’UTR
17421 cg01050273 -0.2598 0.0545 0.0000019 –+ 0.1315697 0.7064011 chr14 101120705
129233 cg08528486 0.1663 0.0350 0.0000021 -+- 0.1315697 0.7894183 chr13 113648767 MCF2L;MCF2L Body;Body
248565 cg17342864 0.1239 0.0268 0.0000036 ++- 0.1950905 1.0000000 chr2 239973967 HDAC4 3’UTR
39707 cg02483029 0.3626 0.0795 0.0000051 ++- 0.2263687 1.0000000 chr8 48297271 KIAA0146 Body
359036 cg26299756 0.2130 0.0468 0.0000054 +++ 0.2263687 1.0000000 chr6 85478807
73319 cg04685632 -0.1960 0.0437 0.0000073 0.2749002 1.0000000 chr20 62082611 KCNQ2;KCNQ2;KCNQ2;KCNQ2;KCNQ2 Body;Body;Body;Body;Body
182880 cg12547807 -0.2121 0.0478 0.0000090 0.2996167 1.0000000 chr1 9473751
46132 cg02892755 -0.2760 0.0627 0.0000106 0.2996167 1.0000000 chr1 28103358 STX12 Body
233149 cg16190478 0.2482 0.0566 0.0000118 +++ 0.2996167 1.0000000 chr21 45789122 TRPM2 Body
20130 cg01218206 -0.2722 0.0621 0.0000118 0.2996167 1.0000000 chr11 116933977 SIK3 Body
138847 cg09233730 0.1233 0.0281 0.0000119 ++- 0.2996167 1.0000000 chr1 1688446 NADK Body
290023 cg20692268 -0.2330 0.0538 0.0000146 0.3155846 1.0000000 chr1 25358981
295061 cg21122375 -0.2208 0.0510 0.0000151 +– 0.3155846 1.0000000 chr7 37956869 SFRP4 TSS1500
3844 cg00226545 0.4875 0.1129 0.0000158 +++ 0.3155846 1.0000000 chr16 54320225 IRX3;IRX3 5’UTR;1stExon
297084 cg21264207 0.2006 0.0465 0.0000159 +++ 0.3155846 1.0000000 chr10 64576130 EGR2;EGR2;EGR2;EGR2 TSS200;5’UTR;TSS200;TSS200
225228 cg15572907 0.4507 0.1050 0.0000175 +++ 0.3173342 1.0000000 chr19 40995921 SPTBN4 Body
220977 cg15206981 -0.1814 0.0423 0.0000177 0.3173342 1.0000000 chr4 124323013 SPRY1;SPRY1 Body;Body
252559 cg17679619 -0.2640 0.0617 0.0000190 0.3250364 1.0000000 chr4 74542972
110843 cg07242931 0.1968 0.0466 0.0000242 ++- 0.3975311 1.0000000 chr1 26034297 MAN1C1 Body
316408 cg22930549 -0.2602 0.0623 0.0000297 0.4198030 1.0000000 chr14 68779833 RAD51L1;RAD51L1;RAD51L1 Body;Body;Body
330525 cg24029819 0.1850 0.0443 0.0000299 +++ 0.4198030 1.0000000 chr7 157550679 PTPRN2;PTPRN2;PTPRN2 Body;Body;Body
223120 cg15396310 -0.1523 0.0366 0.0000311 0.4198030 1.0000000 chr7 72971398 BCL7B Body
222024 cg15300814 0.1316 0.0316 0.0000312 -++ 0.4198030 1.0000000 chr6 111580238 KIAA1919 TSS1500
244019 cg16994941 -0.1645 0.0395 0.0000315 –+ 0.4198030 1.0000000 chr5 141218887
173665 cg11832210 0.4302 0.1036 0.0000331 +++ 0.4198030 1.0000000 chr10 91295346 SLC16A12 TSS200
80050 cg05137378 0.1421 0.0343 0.0000338 +++ 0.4198030 1.0000000 chr1 58393137 DAB1 5’UTR
187142 cg12890388 0.1242 0.0300 0.0000347 -++ 0.4198030 1.0000000 chr20 10412709 MKKS;MKKS 5’UTR;TSS200
249040 cg17382048 -0.2526 0.0611 0.0000356 0.4198030 1.0000000 chr11 118754386 CXCR5 TSS200
263306 cg18513383 0.1561 0.0380 0.0000397 +++ 0.4277078 1.0000000 chr4 57181518 KIAA1211 Body
110963 cg07252171 0.1291 0.0314 0.0000400 +++ 0.4277078 1.0000000 chr5 573376
182554 cg12518360 -0.1890 0.0461 0.0000408 0.4277078 1.0000000 chr11 92931304 SLC36A4 TSS1500
242633 cg16876219 -0.1940 0.0475 0.0000442 0.4277078 1.0000000 chr3 197222311
139515 cg09275980 0.2946 0.0722 0.0000446 +++ 0.4277078 1.0000000 chr15 25350925 SNORD116-29 TSS1500
168526 cg11434671 -0.1587 0.0389 0.0000453 0.4277078 1.0000000 chr17 74524611 CYGB 3’UTR
126827 cg08354093 0.2571 0.0631 0.0000456 ++- 0.4277078 1.0000000 chr20 23029640 THBD 1stExon
70534 cg04498082 -0.1478 0.0363 0.0000474 0.4277078 1.0000000 chr11 356222
74243 cg04752680 -0.1173 0.0289 0.0000482 0.4277078 1.0000000 chr19 14114100 RFX1 5’UTR
69163 cg04402095 -0.1163 0.0286 0.0000484 0.4277078 1.0000000 chr1 156721844 HDGF;HDGF;HDGF Body;1stExon;TSS1500
196521 cg13586599 0.1198 0.0295 0.0000494 +++ 0.4277078 1.0000000 chr6 25652383 SCGN TSS200
370510 cg27144039 -0.1489 0.0369 0.0000539 0.4277078 1.0000000 chr20 62605308
304157 cg21880328 0.0981 0.0243 0.0000546 +++ 0.4277078 1.0000000 chr7 117514017 CTTNBP2 TSS1500
187085 cg12884605 0.1307 0.0324 0.0000550 -++ 0.4277078 1.0000000 chr12 66123314
27848 cg01729837 0.1537 0.0381 0.0000557 +++ 0.4277078 1.0000000 chr19 719622 PALM;PALM Body;Body
353515 cg25869889 0.1542 0.0383 0.0000576 -++ 0.4277078 1.0000000 chr11 6436464 APBB1;APBB1 5’UTR;5’UTR
245138 cg17083982 0.1892 0.0472 0.0000604 +++ 0.4277078 1.0000000 chr12 57946083 KIF5A Body
372554 cg27305735 0.5261 0.1312 0.0000609 -++ 0.4277078 1.0000000 chr1 247537369
351351 cg25687423 -0.1458 0.0364 0.0000618 0.4277078 1.0000000 chr6 43193521 C6orf108;C6orf108 Body;3’UTR
308288 cg22244986 -0.2426 0.0606 0.0000620 0.4277078 1.0000000 chr1 201405370
376680 cg27618777 -0.2320 0.0580 0.0000631 0.4277078 1.0000000 chr6 32804628 TAP2;TAP2 Body;Body
222274 cg15323873 -0.1528 0.0382 0.0000631 +– 0.4277078 1.0000000 chr10 79650526 DLG5 Body
315429 cg22853526 0.1573 0.0393 0.0000635 ++- 0.4277078 1.0000000 chr1 113216965 MOV10;MOV10 TSS200;TSS200
11514 cg00688297 -0.3468 0.0868 0.0000641 0.4277078 1.0000000 chr8 145752292 LRRC24;MGC70857 5’UTR;3’UTR
374551 cg27455890 0.3364 0.0843 0.0000655 -+- 0.4277078 1.0000000 chr10 118976677
189609 cg13100118 -0.2271 0.0569 0.0000657 0.4277078 1.0000000 chr1 19795369 CAPZB Body
17436 cg01051581 -0.1554 0.0390 0.0000669 0.4280695 1.0000000 chr5 32090639 PDZD2 Body
191378 cg13253153 0.1418 0.0356 0.0000683 ++- 0.4293625 1.0000000 chr11 2826988 KCNQ1;KCNQ1 Body;Body
306721 cg22111078 0.4197 0.1058 0.0000729 +++ 0.4468179 1.0000000 chr5 172655925
350973 cg25652701 0.2459 0.0621 0.0000747 -++ 0.4468179 1.0000000 chr7 105348517 ATXN7L1 Body
278372 cg19739774 -0.2022 0.0511 0.0000766 0.4468179 1.0000000 chr7 7711168 RPA3 5’UTR
270820 cg19131667 -0.1760 0.0445 0.0000779 0.4468179 1.0000000 chr3 17236940 TBC1D5;TBC1D5;TBC1D5 Body;Body;Body
140584 cg09353063 0.1687 0.0427 0.0000779 +++ 0.4468179 1.0000000 chr3 8811092 OXTR;OXTR 1stExon;5’UTR
325184 cg23618638 0.2799 0.0709 0.0000782 ++- 0.4468179 1.0000000 chr7 22123315
324549 cg23558842 0.3019 0.0766 0.0000816 +++ 0.4532511 1.0000000 chr11 15095178 CALCB;CALCB 1stExon;5’UTR
30461 cg01895740 0.1191 0.0303 0.0000834 -++ 0.4532511 1.0000000 chr19 7852739 CLEC4GP1 Body
115584 cg07572317 0.1241 0.0316 0.0000842 -++ 0.4532511 1.0000000 chr10 135029782 KNDC1 Body
207752 cg14276580 -0.1726 0.0439 0.0000855 0.4532511 1.0000000 chr13 40527020
28749 cg01787808 -0.2151 0.0548 0.0000871 0.4532511 1.0000000 chr15 34502580 C15orf29 TSS1500
142227 cg09470219 0.1538 0.0392 0.0000880 -++ 0.4532511 1.0000000 chr16 22378015 CDR2 Body
150380 cg10079131 0.1186 0.0303 0.0000897 +++ 0.4532511 1.0000000 chr11 688397 DEAF1 Body
96562 cg06302806 0.1502 0.0383 0.0000898 -++ 0.4532511 1.0000000 chr20 43939970 RBPJL Body
284248 cg20201957 0.1346 0.0344 0.0000914 +++ 0.4532511 1.0000000 chr17 2603638 KIAA0664 Body
91725 cg05945266 0.1368 0.0350 0.0000919 ++- 0.4532511 1.0000000 chr17 80545020 FOXK2 Body
65453 cg04159878 0.2325 0.0595 0.0000933 -++ 0.4532511 1.0000000 chr1 110179127
4536 cg00268744 0.1620 0.0415 0.0000944 ++- 0.4532511 1.0000000 chr16 68281186 PLA2G15 Body
228569 cg15827214 0.1445 0.0370 0.0000949 -++ 0.4532511 1.0000000 chr8 80522324 STMN2 TSS1500
366745 cg26870057 -0.2425 0.0622 0.0000967 0.4553062 1.0000000 chr2 118947242
301518 cg21648245 -0.2749 0.0706 0.0000988 –+ 0.4553062 1.0000000 chr4 109541405 LOC285456;RPL34;RPL34 Body;TSS1500;TSS1500
97877 cg06399735 0.1720 0.0442 0.0000989 +++ 0.4553062 1.0000000 chr8 18836280 PSD3 Body
276528 cg19599951 -0.2648 0.0682 0.0001020 0.4571093 1.0000000 chr11 118754280 CXCR5 TSS1500
250289 cg17478979 0.1844 0.0475 0.0001022 -++ 0.4571093 1.0000000 chr6 149772150 ZC3H12D Body
186512 cg12835806 -0.1459 0.0376 0.0001045 0.4571093 1.0000000 chr16 2812435 SRRM2 Body
261431 cg18370318 0.1477 0.0381 0.0001063 +++ 0.4571093 1.0000000 chr1 16258580 SPEN Body
17195 cg01036779 -0.1355 0.0350 0.0001064 0.4571093 1.0000000 chr19 6768251 SH2D3A TSS1500
370466 cg27141509 -0.2598 0.0670 0.0001066 –+ 0.4571093 1.0000000 chr10 5886111
254669 cg17854066 0.1884 0.0489 0.0001164 +++ 0.4806260 1.0000000 chr4 55575932 KIT;KIT Body;Body
128249 cg08460812 -0.2211 0.0574 0.0001168 –+ 0.4806260 1.0000000 chr4 109087419 LOC641518;LEF1;LEF1;LEF1;LEF1 TSS1500;Body;Body;Body;Body
227288 cg15720669 0.3590 0.0933 0.0001183 +++ 0.4806260 1.0000000 chr3 138666040 FOXL2;C3orf72 TSS200;TSS200
108350 cg07090074 0.1832 0.0476 0.0001185 +++ 0.4806260 1.0000000 chr16 69457218 CYB5B TSS1500
17258 cg01041239 0.1897 0.0493 0.0001209 ++- 0.4806260 1.0000000 chr18 13222581 C18orf1;C18orf1 5’UTR;5’UTR
198286 cg13692433 0.1526 0.0397 0.0001209 +++ 0.4806260 1.0000000 chr11 112832159 NCAM1;NCAM1;NCAM1;NCAM1;NCAM1;NCAM1 1stExon;5’UTR;5’UTR;1stExon;5’UTR;1stExon
298451 cg21405786 0.1850 0.0481 0.0001210 +++ 0.4806260 1.0000000 chr7 148990485 ZNF783 Body
141105 cg09390241 -0.1942 0.0506 0.0001225 0.4815156 1.0000000 chr4 8174148
199983 cg13802583 0.2841 0.0741 0.0001253 +++ 0.4874441 1.0000000 chr12 130961453 RIMBP2 Body
370211 cg27123273 -0.1284 0.0335 0.0001275 0.4909414 1.0000000 chr16 72405329
76726 cg04911180 -0.2970 0.0776 0.0001295 –+ 0.4916344 1.0000000 chr3 176775716 TBL1XR1 Body
323848 cg23504707 0.1422 0.0372 0.0001304 +++ 0.4916344 1.0000000 chr14 60712563 PPM1A;PPM1A 5’UTR;1stExon

Including buccal

metal_all_noCell = read.table('/Users/annebozack/Documents/arsenic_meta/generic-metal/all_no_cell_common_1204201.tbl', sep = "\t")

metal_all_noCell = metalProcess(metal_all_noCell)

write.csv(metal_all_noCell, '/Users/annebozack/Documents/arsenic_meta/generic-metal/DMP_all_no_cell_common_120420.csv')


# Significant probes

# Nominal P-value
table(metal_all_noCell$P.value < 0.05)
#  FALSE   TRUE 
# 356030  21321 

# FDR
table(metal_all_noCell$P.FDR < 0.05)
# FALSE 
# 377351 

table(metal_all_noCell$P.FDR < 0.1)
#  FALSE   TRUE 
#  377348    3 

# Bonferroni
table(metal_all_noCell$P.Bonf < 0.05)
# FALSE 
# 377351  


# GO analysis, FDR < 0.1 probes

annAll2 = rbind(ann850k[,c('Name', 'chr', 'pos', "UCSC_RefGene_Name", "UCSC_RefGene_Group")], ann450kUnique[,c('Name', 'chr', 'pos', "UCSC_RefGene_Name", "UCSC_RefGene_Group")])

go_metal_all_noCell = gometh(sig.cpg = metal_all_noCell$Name[metal_all_noCell$P.FDR < 0.1], all.cpg = metal_all_noCell$Name, array.type = '450K', anno = annAll2)
go_metal_all_noCell = go_metal_all_noCell[order(go_metal_all_noCell$P.DE),]

table(go_metal_all_noCell$P.DE<0.05)
# FALSE  TRUE 
# 22516    46

table(go_metal_all_noCell$FDR<0.05)
# FALSE 
# 22557 

write.csv(go_metal_all_noCell[go_metal_all_noCell$P.DE<0.05,], '/Users/annebozack/Documents/arsenic_meta/generic-metal/GO_DMP_all_no_cell_common_120420.csv')


# KEGG analysis, FDR < 0.1 probes

kegg_metal_all_noCell = gometh(sig.cpg = metal_all_noCell$Name[metal_all_noCell$P.FDR < 0.1], all.cpg = metal_all_noCell$Name, collection = 'KEGG', array.type = '450K', anno = annAll2)
kegg_metal_all_noCell = kegg_metal_all_noCell[order(kegg_metal_all_noCell$P.DE),]

table(kegg_metal_all_noCell$P.DE<0.05)
# FALSE  TRUE 
# 338     2 

table(kegg_metal_all_noCell$FDR<0.05)
# FALSE 
# 340

write.csv(kegg_metal_all_noCell[kegg_metal_all_noCell$P.DE<0.05,], '/Users/annebozack/Documents/arsenic_meta/generic-metal/KEGG_DMP_all_no_cell_common_120420.csv')


# Plotting

gg_qqplot(metal_all_noCell$P.value)
quartz.save('qq_metal_all_noCell_120420.png', type = "png", dpi = 300)

manhattan_meta(metal_all_noCell)
quartz.save('manhattan_metal_all_noCell_120420.png', type = "png", dpi = 300)

volcano_meta(metal_all_noCell)
quartz.save('volcano_metal_all_noCell_120420.png', type = "png", dpi = 300)
knitr::include_graphics("/Users/annebozack/Documents/arsenic_meta/generic-metal/qq_metal_all_noCell_120420.png")

knitr::include_graphics("/Users/annebozack/Documents/arsenic_meta/generic-metal/manhattan_metal_all_noCell_120420.png")

knitr::include_graphics("/Users/annebozack/Documents/arsenic_meta/generic-metal/volcano_metal_all_noCell_120420.png")

Top 100 probes

X Description N DE P.DE FDR
1 path:hsa00565 Ether lipid metabolism 49 1 0.0039233 1
2 path:hsa00564 Glycerophospholipid metabolism 92 1 0.0156145 1
NA NA NA NA NA NA NA
NA.1 NA NA NA NA NA NA
NA.2 NA NA NA NA NA NA
NA.3 NA NA NA NA NA NA
NA.4 NA NA NA NA NA NA
NA.5 NA NA NA NA NA NA
NA.6 NA NA NA NA NA NA
NA.7 NA NA NA NA NA NA
NA.8 NA NA NA NA NA NA
NA.9 NA NA NA NA NA NA
NA.10 NA NA NA NA NA NA
NA.11 NA NA NA NA NA NA
NA.12 NA NA NA NA NA NA
NA.13 NA NA NA NA NA NA
NA.14 NA NA NA NA NA NA
NA.15 NA NA NA NA NA NA
NA.16 NA NA NA NA NA NA
NA.17 NA NA NA NA NA NA
NA.18 NA NA NA NA NA NA
NA.19 NA NA NA NA NA NA
NA.20 NA NA NA NA NA NA
NA.21 NA NA NA NA NA NA
NA.22 NA NA NA NA NA NA
NA.23 NA NA NA NA NA NA
NA.24 NA NA NA NA NA NA
NA.25 NA NA NA NA NA NA
NA.26 NA NA NA NA NA NA
NA.27 NA NA NA NA NA NA
NA.28 NA NA NA NA NA NA
NA.29 NA NA NA NA NA NA
NA.30 NA NA NA NA NA NA
NA.31 NA NA NA NA NA NA
NA.32 NA NA NA NA NA NA
NA.33 NA NA NA NA NA NA
NA.34 NA NA NA NA NA NA
NA.35 NA NA NA NA NA NA
NA.36 NA NA NA NA NA NA
NA.37 NA NA NA NA NA NA
NA.38 NA NA NA NA NA NA
NA.39 NA NA NA NA NA NA
NA.40 NA NA NA NA NA NA
NA.41 NA NA NA NA NA NA
NA.42 NA NA NA NA NA NA
NA.43 NA NA NA NA NA NA
NA.44 NA NA NA NA NA NA
NA.45 NA NA NA NA NA NA
NA.46 NA NA NA NA NA NA
NA.47 NA NA NA NA NA NA
NA.48 NA NA NA NA NA NA
NA.49 NA NA NA NA NA NA
NA.50 NA NA NA NA NA NA
NA.51 NA NA NA NA NA NA
NA.52 NA NA NA NA NA NA
NA.53 NA NA NA NA NA NA
NA.54 NA NA NA NA NA NA
NA.55 NA NA NA NA NA NA
NA.56 NA NA NA NA NA NA
NA.57 NA NA NA NA NA NA
NA.58 NA NA NA NA NA NA
NA.59 NA NA NA NA NA NA
NA.60 NA NA NA NA NA NA
NA.61 NA NA NA NA NA NA
NA.62 NA NA NA NA NA NA
NA.63 NA NA NA NA NA NA
NA.64 NA NA NA NA NA NA
NA.65 NA NA NA NA NA NA
NA.66 NA NA NA NA NA NA
NA.67 NA NA NA NA NA NA
NA.68 NA NA NA NA NA NA
NA.69 NA NA NA NA NA NA
NA.70 NA NA NA NA NA NA
NA.71 NA NA NA NA NA NA
NA.72 NA NA NA NA NA NA
NA.73 NA NA NA NA NA NA
NA.74 NA NA NA NA NA NA
NA.75 NA NA NA NA NA NA
NA.76 NA NA NA NA NA NA
NA.77 NA NA NA NA NA NA
NA.78 NA NA NA NA NA NA
NA.79 NA NA NA NA NA NA
NA.80 NA NA NA NA NA NA
NA.81 NA NA NA NA NA NA
NA.82 NA NA NA NA NA NA
NA.83 NA NA NA NA NA NA
NA.84 NA NA NA NA NA NA
NA.85 NA NA NA NA NA NA
NA.86 NA NA NA NA NA NA
NA.87 NA NA NA NA NA NA
NA.88 NA NA NA NA NA NA
NA.89 NA NA NA NA NA NA
NA.90 NA NA NA NA NA NA
NA.91 NA NA NA NA NA NA
NA.92 NA NA NA NA NA NA
NA.93 NA NA NA NA NA NA
NA.94 NA NA NA NA NA NA
NA.95 NA NA NA NA NA NA
NA.96 NA NA NA NA NA NA
NA.97 NA NA NA NA NA NA

Top 100 GO terms

X ONTOLOGY TERM N DE P.DE FDR
1 GO:0047191 MF 1-alkylglycerophosphocholine O-acyltransferase activity 1 1 0.0009633 1
2 GO:2001246 BP negative regulation of phosphatidylcholine biosynthetic process 1 1 0.0009633 1
3 GO:0047159 MF 1-alkenylglycerophosphocholine O-acyltransferase activity 2 1 0.0009633 1
4 GO:0050200 MF plasmalogen synthase activity 2 1 0.0009633 1
5 GO:0047192 MF 1-alkylglycerophosphocholine O-acetyltransferase activity 3 1 0.0010256 1
6 GO:0047184 MF 1-acylglycerophosphocholine O-acyltransferase activity 4 1 0.0010256 1
7 GO:0016413 MF O-acetyltransferase activity 7 1 0.0014116 1
8 GO:2001245 BP regulation of phosphatidylcholine biosynthetic process 5 1 0.0016745 1
9 GO:0036148 BP phosphatidylglycerol acyl-chain remodeling 18 1 0.0018954 1
10 GO:0043129 BP surfactant homeostasis 9 1 0.0020195 1
11 GO:0048875 BP chemical homeostasis within a tissue 11 1 0.0020229 1
12 GO:0036151 BP phosphatidylcholine acyl-chain remodeling 29 1 0.0027444 1
13 GO:0150172 BP regulation of phosphatidylcholine metabolic process 8 1 0.0029006 1
14 GO:0003841 MF 1-acylglycerol-3-phosphate O-acyltransferase activity 13 1 0.0038687 1
15 GO:0016411 MF acylglycerol O-acyltransferase activity 19 1 0.0038688 1
16 GO:0046471 BP phosphatidylglycerol metabolic process 33 1 0.0040670 1
17 GO:0071072 BP negative regulation of phospholipid biosynthetic process 7 1 0.0042526 1
18 GO:0042171 MF lysophosphatidic acid acyltransferase activity 15 1 0.0043004 1
19 GO:0071617 MF lysophospholipid acyltransferase activity 17 1 0.0043626 1
20 GO:0035577 CC azurophil granule membrane 54 1 0.0048208 1
21 GO:0008374 MF O-acyltransferase activity 42 1 0.0058474 1
22 GO:0071071 BP regulation of phospholipid biosynthetic process 19 1 0.0063761 1
23 GO:1903726 BP negative regulation of phospholipid metabolic process 13 1 0.0063958 1
24 GO:0006656 BP phosphatidylcholine biosynthetic process 38 1 0.0076155 1
25 GO:0016407 MF acetyltransferase activity 92 1 0.0080324 1
26 GO:0006654 BP phosphatidic acid biosynthetic process 47 1 0.0099298 1
27 GO:0051055 BP negative regulation of lipid biosynthetic process 54 1 0.0099924 1
28 GO:0046473 BP phosphatidic acid metabolic process 49 1 0.0104286 1
29 GO:0005811 CC lipid droplet 85 1 0.0106104 1
30 GO:0046470 BP phosphatidylcholine metabolic process 86 1 0.0123996 1
31 GO:0005766 CC primary lysosome 142 1 0.0138020 1
32 GO:0042582 CC azurophil granule 142 1 0.0138020 1
33 GO:0045833 BP negative regulation of lipid metabolic process 93 1 0.0165409 1
34 GO:0016747 MF transferase activity, transferring acyl groups other than amino-acyl groups 200 1 0.0197092 1
35 GO:0016746 MF transferase activity, transferring acyl groups 228 1 0.0214958 1
36 GO:1903725 BP regulation of phospholipid metabolic process 90 1 0.0237582 1
37 GO:0046890 BP regulation of lipid biosynthetic process 197 1 0.0338788 1
38 GO:0060041 BP retina development in camera-type eye 147 1 0.0369490 1
39 GO:0046474 BP glycerophospholipid biosynthetic process 218 1 0.0376870 1
40 GO:0045732 BP positive regulation of protein catabolic process 209 1 0.0380340 1
41 GO:0008654 BP phospholipid biosynthetic process 259 1 0.0413918 1
42 GO:0045017 BP glycerolipid biosynthetic process 251 1 0.0431814 1
43 GO:0030667 CC secretory granule membrane 292 1 0.0436461 1
44 GO:0001894 BP tissue homeostasis 246 1 0.0447369 1
45 GO:0005765 CC lysosomal membrane 353 1 0.0484312 1
46 GO:0098852 CC lytic vacuole membrane 353 1 0.0484312 1
NA NA NA NA NA NA NA NA
NA.1 NA NA NA NA NA NA NA
NA.2 NA NA NA NA NA NA NA
NA.3 NA NA NA NA NA NA NA
NA.4 NA NA NA NA NA NA NA
NA.5 NA NA NA NA NA NA NA
NA.6 NA NA NA NA NA NA NA
NA.7 NA NA NA NA NA NA NA
NA.8 NA NA NA NA NA NA NA
NA.9 NA NA NA NA NA NA NA
NA.10 NA NA NA NA NA NA NA
NA.11 NA NA NA NA NA NA NA
NA.12 NA NA NA NA NA NA NA
NA.13 NA NA NA NA NA NA NA
NA.14 NA NA NA NA NA NA NA
NA.15 NA NA NA NA NA NA NA
NA.16 NA NA NA NA NA NA NA
NA.17 NA NA NA NA NA NA NA
NA.18 NA NA NA NA NA NA NA
NA.19 NA NA NA NA NA NA NA
NA.20 NA NA NA NA NA NA NA
NA.21 NA NA NA NA NA NA NA
NA.22 NA NA NA NA NA NA NA
NA.23 NA NA NA NA NA NA NA
NA.24 NA NA NA NA NA NA NA
NA.25 NA NA NA NA NA NA NA
NA.26 NA NA NA NA NA NA NA
NA.27 NA NA NA NA NA NA NA
NA.28 NA NA NA NA NA NA NA
NA.29 NA NA NA NA NA NA NA
NA.30 NA NA NA NA NA NA NA
NA.31 NA NA NA NA NA NA NA
NA.32 NA NA NA NA NA NA NA
NA.33 NA NA NA NA NA NA NA
NA.34 NA NA NA NA NA NA NA
NA.35 NA NA NA NA NA NA NA
NA.36 NA NA NA NA NA NA NA
NA.37 NA NA NA NA NA NA NA
NA.38 NA NA NA NA NA NA NA
NA.39 NA NA NA NA NA NA NA
NA.40 NA NA NA NA NA NA NA
NA.41 NA NA NA NA NA NA NA
NA.42 NA NA NA NA NA NA NA
NA.43 NA NA NA NA NA NA NA
NA.44 NA NA NA NA NA NA NA
NA.45 NA NA NA NA NA NA NA
NA.46 NA NA NA NA NA NA NA
NA.47 NA NA NA NA NA NA NA
NA.48 NA NA NA NA NA NA NA
NA.49 NA NA NA NA NA NA NA
NA.50 NA NA NA NA NA NA NA
NA.51 NA NA NA NA NA NA NA
NA.52 NA NA NA NA NA NA NA
NA.53 NA NA NA NA NA NA NA

With cell type adjustment

Blood only

metal_blood_cell = read.table('/Users/annebozack/Documents/arsenic_meta/generic-metal/blood_cell_common_1204201.tbl', sep = "\t")

metal_blood_cell = metalProcess(metal_blood_cell)

write.csv(metal_blood_cell, '/Users/annebozack/Documents/arsenic_meta/generic-metal/DMP_blood_cell_common_120420.csv')


# Significant probes

# Nominal P-value
table(metal_blood_cell$P.value < 0.05)
#  FALSE   TRUE 
# 353990  23361 

# FDR
table(metal_blood_cell$P.FDR < 0.05)
#  FALSE   TRUE 
# 377350      1 

table(metal_blood_cell$P.FDR < 0.1)
#  FALSE   TRUE 
# 377343      8

# Bonferroni
table(metal_blood_cell$P.Bonf < 0.05)
#  FALSE   TRUE 
#  377350      1 


# GO analysis, nominally-significant probes

go_metal_blood_cell = gometh(sig.cpg = metal_blood_cell$Name[metal_blood_cell$P.FDR < 0.1], all.cpg = metal_blood_cell$Name, array.type = '450K', sig.genes = T, anno = annAll2)
go_metal_blood_cell = go_metal_blood_cell[order(go_metal_blood_cell$P.DE),]

table(go_metal_blood_cell$P.DE<0.05)
# FALSE  TRUE 
# 22131   452

table(go_metal_blood_cell$FDR<0.05)
# FALSE 
# 22583 

write.csv(go_metal_blood_cell[go_metal_blood_cell$P.DE<0.05,], '/Users/annebozack/Documents/arsenic_meta/generic-metal/GO_DMP_blood_cell_common_120420.csv')


# KEGG analysis, nominally-significant probes

kegg_metal_blood_cell = gometh(sig.cpg = metal_blood_cell$Name[metal_blood_cell$P.FDR < 0.1], all.cpg = metal_blood_cell$Name, array.type = '450K', collection = 'KEGG', sig.genes = T, anno = annAll2)
kegg_metal_blood_cell = kegg_metal_blood_cell[order(kegg_metal_blood_cell$P.DE),]

table(kegg_metal_blood_cell$P.DE<0.05)
# FALSE  TRUE 
# 337     3 

table(kegg_metal_blood_cell$FDR<0.05)
# FALSE 
  # 340

write.csv(kegg_metal_blood_cell[c(1:20),], '/Users/annebozack/Documents/arsenic_meta/generic-metal/KEGG_DMP_blood_cell_common_120420.csv')



# Plotting

gg_qqplot(metal_blood_cell$P.value)
quartz.save('qq_metal_blood_cell_120420.png', type = "png", dpi = 300)

manhattan_meta(metal_blood_cell)
quartz.save('manhattan_metal_blood_cell_120420.png', type = "png", dpi = 300)

volcano_meta(metal_blood_cell)
quartz.save('volcano_metal_blood_cell_120420.png', type = "png", dpi = 300)
knitr::include_graphics("/Users/annebozack/Documents/arsenic_meta/generic-metal/qq_metal_blood_cell_120420.png")

knitr::include_graphics("/Users/annebozack/Documents/arsenic_meta/generic-metal/manhattan_metal_blood_cell_120420.png")

knitr::include_graphics("/Users/annebozack/Documents/arsenic_meta/generic-metal/volcano_metal_blood_cell_120420.png")

Top 100 probes

X Name Effect StdErr P.value Direction P.FDR P.Bonf chr pos UCSC_RefGene_Name UCSC_RefGene_Group
194923 cg13490635 0.3069 0.0567 1.00e-07 +++ 0.0237656 0.0237656 chr8 30242021 RBPMS;RBPMS;RBPMS;RBPMS;RBPMS;RBPMS;RBPMS;RBPMS 5’UTR;5’UTR;1stExon;1stExon;1stExon;5’UTR;1stExon;5’UTR
186512 cg12835806 -0.2055 0.0408 5.00e-07 0.0861304 0.1819964 chr16 2812435 SRRM2 Body
143925 cg09595163 0.5056 0.1019 7.00e-07 +++ 0.0861304 0.2655796 chr3 55515541 WNT5A Body
360597 cg26412543 -0.2648 0.0540 1.00e-06 0.0861304 0.3598419 chr6 32128829 PPT2;PPT2 Body;Body
44706 cg02799448 0.1687 0.0351 1.50e-06 -++ 0.0861304 0.5607436 chr6 137817008 OLIG3 TSS1500
95521 cg06218338 0.3073 0.0641 1.60e-06 -++ 0.0861304 0.6181009 chr7 27231894
353232 cg25840057 -0.1794 0.0375 1.70e-06 +– 0.0861304 0.6456476 chr13 113730354 MCF2L;MCF2L Body;Body
220977 cg15206981 -0.2178 0.0456 1.80e-06 0.0861304 0.6890429 chr4 124323013 SPRY1;SPRY1 Body;Body
30961 cg01927825 -0.3417 0.0725 2.50e-06 0.1032265 0.9290382 chr1 2121724 C1orf86;LOC100128003;C1orf86 Body;Body;Body
222521 cg15345437 -0.1694 0.0362 2.90e-06 0.1046133 1.0000000 chr11 62620843 SNORD22;SNORD31;SNHG1 TSS1500;Body;Body
201470 cg13900348 0.3509 0.0755 3.40e-06 +++ 0.1046133 1.0000000 chr5 76114646 F2RL1 TSS200
20130 cg01218206 -0.2163 0.0467 3.60e-06 0.1046133 1.0000000 chr11 116933977 SIK3 Body
286295 cg20380069 0.1757 0.0379 3.60e-06 +++ 0.1046133 1.0000000 chr12 120806617 MSI1 Body
2859 cg00160440 -0.1362 0.0297 4.50e-06 0.1202402 1.0000000 chr4 134077575 PCDH10 Body
64145 cg04080022 -0.1951 0.0430 5.80e-06 0.1363416 1.0000000 chr16 89648534 CPNE7;CPNE7 Body;Body
96670 cg06313349 -0.2251 0.0496 5.80e-06 0.1363416 1.0000000 chr7 157494424 PTPRN2;PTPRN2;PTPRN2 Body;Body;Body
173665 cg11832210 0.4809 0.1069 6.80e-06 +++ 0.1513178 1.0000000 chr10 91295346 SLC16A12 TSS200
48278 cg03025061 -0.1950 0.0437 8.00e-06 0.1566950 1.0000000 chr8 109261275 EIF3E TSS1500
184123 cg12637057 0.2537 0.0569 8.10e-06 +++ 0.1566950 1.0000000 chr20 59967284 CDH4 Body
145527 cg09714379 0.2894 0.0649 8.30e-06 +++ 0.1566950 1.0000000 chr10 135044040 UTF1 1stExon
35348 cg02206980 -0.5285 0.1199 1.04e-05 0.1855881 1.0000000 chr6 13574034 SIRT5;SIRT5 TSS1500;TSS1500
176796 cg12065616 -0.1729 0.0393 1.08e-05 0.1855881 1.0000000 chr12 94954828
61580 cg03906434 0.3445 0.0794 1.45e-05 -++ 0.2168360 1.0000000 chr7 27231819
114412 cg07492924 -0.3742 0.0863 1.47e-05 0.2168360 1.0000000 chr16 433825 LOC100134368 Body
291217 cg20784693 -0.5836 0.1347 1.47e-05 0.2168360 1.0000000 chr2 239984030 HDAC4 Body
85525 cg05507514 -0.1798 0.0416 1.55e-05 0.2168360 1.0000000 chr3 153842846 SGEF Body
50150 cg03149958 -0.1844 0.0427 1.58e-05 0.2168360 1.0000000 chr6 36326677
279928 cg19851029 0.1962 0.0456 1.68e-05 +++ 0.2168360 1.0000000 chr3 138669137 C3orf72 Body
178323 cg12174276 0.1279 0.0297 1.69e-05 +++ 0.2168360 1.0000000 chr6 166401921 LOC441177;C6orf176;C6orf176 Body;TSS1500;TSS1500
200512 cg13837335 -0.1365 0.0319 1.81e-05 0.2168360 1.0000000 chr9 2191798 SMARCA2;SMARCA2 Body;Body
133800 cg08856347 0.2545 0.0596 1.94e-05 +++ 0.2168360 1.0000000 chr2 289390 FAM150B TSS1500
187357 cg12908187 0.1873 0.0439 1.94e-05 -++ 0.2168360 1.0000000 chr16 88450261
373928 cg27406919 -0.1801 0.0422 1.95e-05 0.2168360 1.0000000 chr16 87212733
201996 cg13928490 -0.2502 0.0586 1.95e-05 0.2168360 1.0000000 chr13 51640442 GUCY1B2 TSS200
46686 cg02925222 0.1116 0.0264 2.29e-05 +++ 0.2168360 1.0000000 chr11 280445 NLRP6 Body
92037 cg05965902 0.1887 0.0446 2.31e-05 +++ 0.2168360 1.0000000 chr13 21635727 LATS2 TSS200
23933 cg01464730 -0.7699 0.1821 2.35e-05 0.2168360 1.0000000 chr17 78809873 RPTOR;RPTOR Body;Body
168281 cg11414610 -0.1493 0.0353 2.38e-05 0.2168360 1.0000000 chr19 16528319 EPS15L1 Body
254158 cg17819053 0.1555 0.0368 2.38e-05 +++ 0.2168360 1.0000000 chr1 119549626
347007 cg25330878 -0.1506 0.0357 2.48e-05 0.2168360 1.0000000 chr17 17379109 MED9 TSS1500
131753 cg08706492 0.2375 0.0564 2.57e-05 +++ 0.2168360 1.0000000 chr1 247374357
4731 cg00284153 -0.1746 0.0415 2.57e-05 0.2168360 1.0000000 chr10 135171713 C10orf125;C10orf125 TSS200;TSS200
306721 cg22111078 0.4708 0.1119 2.60e-05 +++ 0.2168360 1.0000000 chr5 172655925
198286 cg13692433 0.1821 0.0433 2.65e-05 +++ 0.2168360 1.0000000 chr11 112832159 NCAM1;NCAM1;NCAM1;NCAM1;NCAM1;NCAM1 1stExon;5’UTR;5’UTR;1stExon;5’UTR;1stExon
282053 cg20011402 0.3952 0.0941 2.66e-05 +++ 0.2168360 1.0000000 chr10 17496239 ST8SIA6 1stExon
236494 cg16427033 -0.1492 0.0355 2.70e-05 +– 0.2168360 1.0000000 chr10 109023583
363371 cg26623444 0.1747 0.0416 2.73e-05 +++ 0.2168360 1.0000000 chr7 31376092
228619 cg15830431 0.1666 0.0398 2.78e-05 ++- 0.2168360 1.0000000 chr8 99952591
166619 cg11289100 0.2363 0.0565 2.86e-05 +++ 0.2168360 1.0000000 chr17 19313024 RNF112 TSS1500
199780 cg13791254 0.5591 0.1338 2.93e-05 -++ 0.2168360 1.0000000 chr9 100616607 FOXE1 1stExon
321357 cg23300529 -0.1586 0.0380 3.01e-05 0.2168360 1.0000000 chr8 21989012 HR;HR TSS1500;TSS1500
353248 cg25840780 -0.3055 0.0733 3.12e-05 0.2168360 1.0000000 chr20 50156843 NFATC2;NFATC2;NFATC2 Body;Body;Body
193620 cg13415566 -0.3939 0.0947 3.18e-05 0.2168360 1.0000000 chr10 125423240
295061 cg21122375 -0.2285 0.0550 3.22e-05 0.2168360 1.0000000 chr7 37956869 SFRP4 TSS1500
312496 cg22621867 0.3367 0.0811 3.27e-05 +++ 0.2168360 1.0000000 chr3 51990301 GPR62 1stExon
291688 cg20824761 0.5956 0.1434 3.28e-05 +++ 0.2168360 1.0000000 chr15 69591567 PAQR5 5’UTR
250912 cg17523124 0.1690 0.0408 3.40e-05 +++ 0.2168360 1.0000000 chr20 24451769 TMEM90B 5’UTR
304218 cg21885638 -0.1303 0.0315 3.45e-05 0.2168360 1.0000000 chr3 129306552 PLXND1 Body
72911 cg04658543 0.2106 0.0509 3.51e-05 +++ 0.2168360 1.0000000 chr12 113904848 LHX5 Body
118338 cg07766612 0.4675 0.1131 3.57e-05 +++ 0.2168360 1.0000000 chr1 26372887 SLC30A2;SLC30A2 TSS1500;TSS1500
265230 cg18672986 0.3001 0.0727 3.66e-05 +++ 0.2168360 1.0000000 chr19 35521772 SCN1B;SCN1B Body;Body
110684 cg07232688 -0.1766 0.0428 3.66e-05 0.2168360 1.0000000 chr1 100644688 LRRC39 TSS1500
316250 cg22915154 -0.2157 0.0523 3.69e-05 0.2168360 1.0000000 chr11 68816030 TPCN2 TSS1500
292390 cg20899625 -0.1458 0.0354 3.78e-05 0.2168360 1.0000000 chr3 126721131 PLXNA1 Body
180848 cg12392225 -0.1565 0.0380 3.79e-05 0.2168360 1.0000000 chr2 3464066 TTC15 Body
86791 cg05600350 0.4214 0.1023 3.82e-05 +++ 0.2168360 1.0000000 chr4 4858598
295936 cg21185289 0.4583 0.1113 3.85e-05 +++ 0.2168360 1.0000000 chr2 74743437 TLX2 3’UTR
225228 cg15572907 0.4958 0.1206 3.97e-05 +++ 0.2171135 1.0000000 chr19 40995921 SPTBN4 Body
354980 cg25996001 -0.1629 0.0396 3.97e-05 0.2171135 1.0000000 chr15 23003087 CYFIP1;CYFIP1 3’UTR;3’UTR
73319 cg04685632 -0.1611 0.0393 4.15e-05 0.2178127 1.0000000 chr20 62082611 KCNQ2;KCNQ2;KCNQ2;KCNQ2;KCNQ2 Body;Body;Body;Body;Body
343981 cg25076597 -0.3534 0.0862 4.15e-05 0.2178127 1.0000000 chr10 134150581 LRRC27;LRRC27;LRRC27;LRRC27;LRRC27 Body;TSS200;Body;Body;Body
90057 cg05837401 0.2287 0.0558 4.17e-05 +++ 0.2178127 1.0000000 chr3 125899086 ALDH1L1 5’UTR
5363 cg00321074 -0.1290 0.0316 4.41e-05 0.2178127 1.0000000 chr3 19990693 RAB5A 5’UTR
136595 cg09064848 0.2053 0.0503 4.41e-05 +++ 0.2178127 1.0000000 chr17 3627007 ITGAE;GSG2 Body;TSS200
219413 cg15083775 0.1410 0.0345 4.42e-05 –+ 0.2178127 1.0000000 chr17 48054048
297867 cg21344215 0.1552 0.0380 4.47e-05 +++ 0.2178127 1.0000000 chr2 27851972 GPN1;CCDC121;CCDC121;GPN1;CCDC121;GPN1;GPN1;GPN1 5’UTR;TSS1500;TSS200;Body;TSS1500;5’UTR;Body;1stExon
5575 cg00333154 0.3250 0.0797 4.53e-05 +++ 0.2178127 1.0000000 chr6 106808703
2422 cg00133970 -0.2104 0.0516 4.56e-05 0.2178127 1.0000000 chr7 44123200 POLM TSS1500
214534 cg14709833 0.3309 0.0812 4.56e-05 +++ 0.2178127 1.0000000 chr13 112157732
34800 cg02166532 0.1862 0.0457 4.68e-05 +++ 0.2207503 1.0000000 chr11 2159853 INS-IGF2;IGF2;IGF2;IGF2;IGF2 Body;Body;5’UTR;5’UTR;1stExon
260043 cg18259339 -0.2166 0.0534 4.96e-05 0.2260924 1.0000000 chr17 76441793 DNAH17 Body
168429 cg11425470 -0.1835 0.0452 4.97e-05 0.2260924 1.0000000 chr1 109271795 FNDC7 Body
324549 cg23558842 0.3088 0.0761 4.97e-05 +++ 0.2260924 1.0000000 chr11 15095178 CALCB;CALCB 1stExon;5’UTR
331371 cg24090911 -0.2089 0.0516 5.13e-05 0.2273111 1.0000000 chr5 400732 AHRR Body
180577 cg12368188 0.3807 0.0941 5.17e-05 +++ 0.2273111 1.0000000 chr15 67326082
93 cg00004257 0.2348 0.0580 5.19e-05 +++ 0.2273111 1.0000000 chr1 34629175 CSMD2 Body
18568 cg01117452 -0.1664 0.0412 5.27e-05 0.2273111 1.0000000 chr14 72703626 RGS6 Body
307232 cg22153116 0.1627 0.0402 5.30e-05 -++ 0.2273111 1.0000000 chr9 15306736 TTC39B;TTC39B;TTC39B;TTC39B Body;Body;Body;Body
351351 cg25687423 -0.1654 0.0412 5.82e-05 0.2419608 1.0000000 chr6 43193521 C6orf108;C6orf108 Body;3’UTR
301289 cg21629895 -0.1786 0.0444 5.82e-05 0.2419608 1.0000000 chr2 25565795 DNMT3A;DNMT3A;DNMT3A TSS1500;TSS1500;TSS1500
153656 cg10308749 -0.3923 0.0976 5.84e-05 0.2419608 1.0000000 chr6 126080335 HEY2 Body
199878 cg13797073 -0.2046 0.0509 5.93e-05 0.2431043 1.0000000 chr9 71199964
139515 cg09275980 0.3030 0.0755 6.04e-05 +++ 0.2449941 1.0000000 chr15 25350925 SNORD116-29 TSS1500
184603 cg12673019 -0.1488 0.0371 6.12e-05 +– 0.2458402 1.0000000 chr11 17939679 SERGEF Body
100076 cg06555468 0.2055 0.0514 6.28e-05 +++ 0.2481358 1.0000000 chr7 2094790 MAD1L1;MAD1L1;MAD1L1 Body;Body;Body
309222 cg22332910 0.2330 0.0582 6.34e-05 +++ 0.2481358 1.0000000 chr11 35641226 FJX1 1stExon
157910 cg10615519 0.4241 0.1061 6.42e-05 +++ 0.2481358 1.0000000 chr12 88974243 KITLG;KITLG TSS200;TSS200
116539 cg07636145 -0.2033 0.0509 6.45e-05 0.2481358 1.0000000 chr16 56228188 DKFZP434H168;GNAO1;GNAO1 Body;Body;Body
131348 cg08680083 -0.2311 0.0579 6.64e-05 0.2481358 1.0000000 chr19 50309143 AP2A1;AP2A1 Body;Body
16383 cg00990385 -0.1788 0.0448 6.70e-05 0.2481358 1.0000000 chr12 113587690 CCDC42B 1stExon

Top 100 GO terms

X ONTOLOGY TERM N DE P.DE FDR SigGenesInSet
GO:0000132 BP establishment of mitotic spindle orientation 30 1 0.0170717 1 SPRY1
GO:0000578 BP embryonic axis specification 36 1 0.0241637 1 WNT5A
GO:0000932 CC P-body 86 1 0.0416833 1 RBPMS
GO:0001654 BP eye development 373 2 0.0283476 1 SPRY1,WNT5A
GO:0001655 BP urogenital system development 320 2 0.0204470 1 SPRY1,WNT5A
GO:0001702 BP gastrulation with mouth forming second 26 1 0.0205125 1 WNT5A
GO:0001708 BP cell fate specification 99 2 0.0032883 1 OLIG3,WNT5A
GO:0001756 BP somitogenesis 67 1 0.0478998 1 WNT5A
GO:0001759 BP organ induction 23 2 0.0002145 1 SPRY1,WNT5A
GO:0001763 BP morphogenesis of a branching structure 195 2 0.0110409 1 SPRY1,WNT5A
GO:0001837 BP epithelial to mesenchymal transition 147 2 0.0044294 1 SPRY1,WNT5A
GO:0001932 BP regulation of protein phosphorylation 1405 3 0.0316030 1 SPRY1,RBPMS,WNT5A
GO:0001947 BP heart looping 62 1 0.0402549 1 WNT5A
GO:0001961 BP positive regulation of cytokine-mediated signaling pathway 49 1 0.0147355 1 WNT5A
GO:0002011 BP morphogenesis of an epithelial sheet 56 1 0.0451227 1 WNT5A
GO:0002053 BP positive regulation of mesenchymal cell proliferation 25 1 0.0307164 1 WNT5A
GO:0002066 BP columnar/cuboidal epithelial cell development 62 1 0.0434813 1 WNT5A
GO:0002067 BP glandular epithelial cell differentiation 48 1 0.0425664 1 WNT5A
GO:0002068 BP glandular epithelial cell development 26 1 0.0248938 1 WNT5A
GO:0002072 BP optic cup morphogenesis involved in camera-type eye development 8 1 0.0105911 1 WNT5A
GO:0002088 BP lens development in camera-type eye 80 2 0.0011900 1 SPRY1,WNT5A
GO:0002367 BP cytokine production involved in immune response 94 1 0.0371153 1 WNT5A
GO:0002687 BP positive regulation of leukocyte migration 131 1 0.0435196 1 WNT5A
GO:0002688 BP regulation of leukocyte chemotaxis 112 1 0.0390771 1 WNT5A
GO:0002690 BP positive regulation of leukocyte chemotaxis 89 1 0.0297444 1 WNT5A
GO:0002700 BP regulation of production of molecular mediator of immune response 130 1 0.0466534 1 WNT5A
GO:0002702 BP positive regulation of production of molecular mediator of immune response 93 1 0.0320167 1 WNT5A
GO:0002718 BP regulation of cytokine production involved in immune response 74 1 0.0341841 1 WNT5A
GO:0002720 BP positive regulation of cytokine production involved in immune response 50 1 0.0216393 1 WNT5A
GO:0003002 BP regionalization 343 2 0.0280862 1 SPRY1,WNT5A
GO:0003007 BP heart morphogenesis 255 2 0.0147387 1 SPRY1,WNT5A
GO:0003128 BP heart field specification 17 1 0.0197641 1 WNT5A
GO:0003129 BP heart induction 10 1 0.0112860 1 WNT5A
GO:0003138 BP primary heart field specification 3 1 0.0039931 1 WNT5A
GO:0003139 BP secondary heart field specification 11 1 0.0124197 1 WNT5A
GO:0003143 BP embryonic heart tube morphogenesis 68 1 0.0462131 1 WNT5A
GO:0003156 BP regulation of animal organ formation 37 2 0.0006690 1 SPRY1,WNT5A
GO:0003209 BP cardiac atrium morphogenesis 30 1 0.0274007 1 WNT5A
GO:0003213 BP cardiac right atrium morphogenesis 2 1 0.0041147 1 WNT5A
GO:0003230 BP cardiac atrium development 36 1 0.0298481 1 WNT5A
GO:0003283 BP atrial septum development 23 1 0.0203575 1 WNT5A
GO:0003306 BP Wnt signaling pathway involved in heart development 13 1 0.0077832 1 WNT5A
GO:0003307 BP regulation of Wnt signaling pathway involved in heart development 9 1 0.0048594 1 WNT5A
GO:0003308 BP negative regulation of Wnt signaling pathway involved in heart development 7 1 0.0033385 1 WNT5A
GO:0003309 BP type B pancreatic cell differentiation 25 1 0.0221791 1 WNT5A
GO:0003323 BP type B pancreatic cell development 20 1 0.0159645 1 WNT5A
GO:0003344 BP pericardium morphogenesis 9 1 0.0086510 1 WNT5A
GO:0003401 BP axis elongation 28 2 0.0003656 1 SPRY1,WNT5A
GO:0003402 BP planar cell polarity pathway involved in axis elongation 6 1 0.0093298 1 WNT5A
GO:0003408 BP optic cup formation involved in camera-type eye development 3 1 0.0040144 1 WNT5A
GO:0003712 MF transcription coregulator activity 462 2 0.0239655 1 RBPMS,OLIG3
GO:0003727 MF single-stranded RNA binding 81 1 0.0376670 1 RBPMS
GO:0003729 MF mRNA binding 491 2 0.0054702 1 RBPMS,SRRM2
GO:0005109 MF frizzled binding 37 1 0.0306569 1 WNT5A
GO:0005115 MF receptor tyrosine kinase-like orphan receptor binding 1 1 0.0020187 1 WNT5A
GO:0005543 MF phospholipid binding 425 2 0.0226882 1 MCF2L,WNT5A
GO:0005681 CC spliceosomal complex 177 1 0.0442644 1 SRRM2
GO:0005684 CC U2-type spliceosomal complex 88 1 0.0244405 1 SRRM2
GO:0006139 BP nucleobase-containing compound metabolic process 5578 5 0.0385323 1 RBPMS,OLIG3,SRRM2,WNT5A,PPT2
GO:0006396 BP RNA processing 1235 2 0.0261175 1 RBPMS,SRRM2
GO:0006582 BP melanin metabolic process 22 1 0.0137342 1 WNT5A
GO:0006637 BP acyl-CoA metabolic process 95 1 0.0343804 1 PPT2
GO:0006725 BP cellular aromatic compound metabolic process 5786 5 0.0436372 1 RBPMS,OLIG3,SRRM2,WNT5A,PPT2
GO:0006793 BP phosphorus metabolic process 3152 4 0.0465551 1 SPRY1,RBPMS,WNT5A,PPT2
GO:0006796 BP phosphate-containing compound metabolic process 3127 4 0.0453948 1 SPRY1,RBPMS,WNT5A,PPT2
GO:0007163 BP establishment or maintenance of cell polarity 214 2 0.0091182 1 SPRY1,WNT5A
GO:0007167 BP enzyme linked receptor protein signaling pathway 1029 3 0.0217499 1 SPRY1,RBPMS,WNT5A
GO:0007178 BP transmembrane receptor protein serine/threonine kinase signaling pathway 341 3 0.0012016 1 SPRY1,RBPMS,WNT5A
GO:0007223 BP Wnt signaling pathway, calcium modulating pathway 38 1 0.0289937 1 WNT5A
GO:0007257 BP activation of JUN kinase activity 38 1 0.0243513 1 WNT5A
GO:0007264 BP small GTPase mediated signal transduction 469 2 0.0393178 1 SPRY1,MCF2L
GO:0007350 BP blastoderm segmentation 20 1 0.0186601 1 WNT5A
GO:0007351 BP tripartite regional subdivision 16 1 0.0140401 1 WNT5A
GO:0007389 BP pattern specification process 436 2 0.0405926 1 SPRY1,WNT5A
GO:0007442 BP hindgut morphogenesis 7 1 0.0094349 1 WNT5A
GO:0007494 BP midgut development 12 1 0.0125057 1 WNT5A
GO:0008143 MF poly(A) binding 21 1 0.0095053 1 RBPMS
GO:0008474 MF palmitoyl-(protein) hydrolase activity 13 1 0.0047432 1 PPT2
GO:0008543 BP fibroblast growth factor receptor signaling pathway 112 2 0.0021005 1 SPRY1,WNT5A
GO:0008595 BP anterior/posterior axis specification, embryo 16 1 0.0140401 1 WNT5A
GO:0009948 BP anterior/posterior axis specification 48 1 0.0317891 1 WNT5A
GO:0010092 BP specification of animal organ identity 35 2 0.0006903 1 SPRY1,WNT5A
GO:0010453 BP regulation of cell fate commitment 37 1 0.0217979 1 WNT5A
GO:0010463 BP mesenchymal cell proliferation 43 1 0.0467404 1 WNT5A
GO:0010464 BP regulation of mesenchymal cell proliferation 33 1 0.0385379 1 WNT5A
GO:0010494 CC cytoplasmic stress granule 69 1 0.0263234 1 RBPMS
GO:0010719 BP negative regulation of epithelial to mesenchymal transition 40 1 0.0284573 1 SPRY1
GO:0010799 BP regulation of peptidyl-threonine phosphorylation 46 1 0.0307112 1 WNT5A
GO:0010800 BP positive regulation of peptidyl-threonine phosphorylation 28 1 0.0185498 1 WNT5A
GO:0010818 BP T cell chemotaxis 22 1 0.0071995 1 WNT5A
GO:0010819 BP regulation of T cell chemotaxis 15 1 0.0049580 1 WNT5A
GO:0010820 BP positive regulation of T cell chemotaxis 14 1 0.0049580 1 WNT5A
GO:0010862 BP positive regulation of pathway-restricted SMAD protein phosphorylation 47 1 0.0192732 1 RBPMS
GO:0010934 BP macrophage cytokine production 15 1 0.0081533 1 WNT5A
GO:0010935 BP regulation of macrophage cytokine production 14 1 0.0078638 1 WNT5A
GO:0015030 CC Cajal body 70 1 0.0124663 1 SRRM2
GO:0016790 MF thiolester hydrolase activity 38 1 0.0128339 1 PPT2
GO:0019748 BP secondary metabolic process 55 1 0.0252502 1 WNT5A
GO:0021517 BP ventral spinal cord development 48 1 0.0444256 1 OLIG3
GO:0021520 BP spinal cord motor neuron cell fate specification 13 1 0.0173372 1 OLIG3

Including buccal

metal_all_cell = read.table('/Users/annebozack/Documents/arsenic_meta/generic-metal/all_cell_common_1204201.tbl', sep = "\t")

metal_all_cell = metalProcess(metal_all_cell)

write.csv(metal_all_cell, '/Users/annebozack/Documents/arsenic_meta/generic-metal/DMP_all_cell_common_120420.csv')


# Significant probes

# Nominal P-value
table(metal_all_cell$P.value < 0.05)
#  FALSE   TRUE 
# 354739  22612

# FDR
table(metal_all_cell$P.FDR < 0.05)
# FALSE   TRUE 
# 377348      3 

table(metal_all_cell$P.FDR < 0.1)
# FALSE   TRUE 
# 377326     25 

# Bonferroni
table(metal_all_cell$P.Bonf < 0.05)
# FALSE 
# 377351 


# GO analysis, nominally-significant probes

go_metal_all_cell = gometh(sig.cpg = metal_all_cell$Name[metal_all_cell$P.FDR < 0.1], all.cpg = metal_all_cell$Name, array.type = '450K', anno = annAll2)
go_metal_all_cell = go_metal_all_cell[order(go_metal_all_cell$P.DE),]

table(go_metal_all_cell$P.DE<0.05)
# FALSE  TRUE 
# 22246   337

table(go_metal_all_cell$FDR<0.05)
# FALSE 
# 22583 

write.csv(go_metal_all_cell[go_metal_all_cell$P.DE<0.05,], '/Users/annebozack/Documents/arsenic_meta/generic-metal/GO_DMP_all_cell_common_120420.csv')


# KEGG analysis, nominally-significant probes

kegg_metal_all_cell = gometh(sig.cpg = metal_all_cell$Name[metal_all_cell$P.FDR < 0.1], all.cpg = metal_all_cell$Name, array.type = '450K', collection = 'KEGG', sig.genes = T, anno = annAll2)
kegg_metal_all_cell = kegg_metal_all_cell[order(kegg_metal_all_cell$P.DE),]

table(kegg_metal_all_cell$P.DE<0.05)
# FALSE  TRUE 
# 335     5 

table(kegg_metal_all_cell$FDR<0.05)
# FALSE 
# 340

write.csv(kegg_metal_all_cell[c(1:20),], '/Users/annebozack/Documents/arsenic_meta/generic-metal/KEGG_DMP_all_cell_common_120420.csv')



# Plotting

gg_qqplot(metal_all_cell$P.value)
quartz.save('qq_metal_all_cell_120420.png', type = "png", dpi = 300)

manhattan_meta(metal_all_cell, FDR=T)
quartz.save('manhattan_metal_all_cell_120420.png', type = "png", dpi = 300)

volcano_meta(metal_all_cell)
quartz.save('volcano_metal_all_cell_120420.png', type = "png", dpi = 300)
knitr::include_graphics("/Users/annebozack/Documents/arsenic_meta/generic-metal/qq_metal_all_cell_120420.png")

knitr::include_graphics("/Users/annebozack/Documents/arsenic_meta/generic-metal/manhattan_metal_all_cell_120420.png")

knitr::include_graphics("/Users/annebozack/Documents/arsenic_meta/generic-metal/volcano_metal_all_cell_120420.png")

Top 100 probes

X Name Effect StdErr P.value Direction P.FDR P.Bonf chr pos UCSC_RefGene_Name UCSC_RefGene_Group
139515 cg09275980 0.3064 0.0594 3.00e-07 ++++ 0.0415715 0.0950925 chr15 25350925 SNORD116-29 TSS1500
291217 cg20784693 -0.6410 0.1252 3.00e-07 —- 0.0415715 0.1162996 chr2 239984030 HDAC4 Body
260100 cg18263451 -0.1213 0.0238 3.00e-07 –+- 0.0415715 0.1247145 chr1 25573180 C1orf63 Body
254158 cg17819053 0.1723 0.0348 7.00e-07 ++++ 0.0603460 0.2826736 chr1 119549626
95521 cg06218338 0.3110 0.0630 8.00e-07 -+++ 0.0603460 0.3017299 chr7 27231894
284743 cg20247661 0.1739 0.0356 1.00e-06 -+++ 0.0633950 0.3890489 chr10 21812368 C10orf140 5’UTR
184123 cg12637057 0.2531 0.0521 1.20e-06 ++++ 0.0633950 0.4437648 chr20 59967284 CDH4 Body
46686 cg02925222 0.1166 0.0242 1.40e-06 ++++ 0.0637723 0.5305555 chr11 280445 NLRP6 Body
90057 cg05837401 0.2379 0.0496 1.60e-06 ++++ 0.0637723 0.6052710 chr3 125899086 ALDH1L1 5’UTR
222521 cg15345437 -0.1530 0.0320 1.70e-06 —- 0.0637723 0.6377232 chr11 62620843 SNORD22;SNORD31;SNHG1 TSS1500;Body;Body
114412 cg07492924 -0.3734 0.0791 2.40e-06 —- 0.0810276 0.8913031 chr16 433825 LOC100134368 Body
143925 cg09595163 0.4584 0.0977 2.70e-06 +++- 0.0832204 1.0000000 chr3 55515541 WNT5A Body
44706 cg02799448 0.1600 0.0342 2.90e-06 -++- 0.0832204 1.0000000 chr6 137817008 OLIG3 TSS1500
194923 cg13490635 0.2316 0.0500 3.50e-06 +++- 0.0931114 1.0000000 chr8 30242021 RBPMS;RBPMS;RBPMS;RBPMS;RBPMS;RBPMS;RBPMS;RBPMS 5’UTR;5’UTR;1stExon;1stExon;1stExon;5’UTR;1stExon;5’UTR
225228 cg15572907 0.5107 0.1105 3.80e-06 ++++ 0.0931114 1.0000000 chr19 40995921 SPTBN4 Body
9270 cg00550554 -0.1879 0.0407 3.90e-06 —- 0.0931114 1.0000000 chr6 30294969 HCG18;TRIM39;HCG18;TRIM39 TSS200;5’UTR;TSS200;TSS200
138010 cg09169455 -0.4663 0.1015 4.30e-06 —- 0.0953755 1.0000000 chr5 16843340 MYO10 Body
360597 cg26412543 -0.2220 0.0485 4.70e-06 —- 0.0953755 1.0000000 chr6 32128829 PPT2;PPT2 Body;Body
363371 cg26623444 0.1849 0.0406 5.10e-06 ++++ 0.0953755 1.0000000 chr7 31376092
30961 cg01927825 -0.2978 0.0654 5.30e-06 —- 0.0953755 1.0000000 chr1 2121724 C1orf86;LOC100128003;C1orf86 Body;Body;Body
343981 cg25076597 -0.3140 0.0690 5.40e-06 —- 0.0953755 1.0000000 chr10 134150581 LRRC27;LRRC27;LRRC27;LRRC27;LRRC27 Body;TSS200;Body;Body;Body
23933 cg01464730 -0.7679 0.1692 5.60e-06 —- 0.0953755 1.0000000 chr17 78809873 RPTOR;RPTOR Body;Body
136234 cg09035938 0.1847 0.0408 6.00e-06 ++++ 0.0953755 1.0000000 chr1 35347799 DLGAP3 Body
33505 cg02081266 0.3474 0.0768 6.10e-06 ++++ 0.0953755 1.0000000 chr17 59529618
277060 cg19640581 -0.2875 0.0638 6.50e-06 —- 0.0977943 1.0000000 chr5 501343 SLC9A3 Body
61580 cg03906434 0.3385 0.0755 7.30e-06 -+++ 0.1050131 1.0000000 chr7 27231819
299146 cg21468180 -0.1345 0.0301 7.80e-06 —- 0.1050131 1.0000000 chr3 13697288 LOC285375 Body
243179 cg16919449 -0.4103 0.0919 8.10e-06 —- 0.1050131 1.0000000 chr10 36054185
373928 cg27406919 -0.1775 0.0399 8.50e-06 —- 0.1050131 1.0000000 chr16 87212733
41431 cg02591871 -0.1270 0.0285 8.60e-06 —- 0.1050131 1.0000000 chr19 14228565 PRKACA TSS200
187357 cg12908187 0.1860 0.0418 8.60e-06 -+++ 0.1050131 1.0000000 chr16 88450261
119415 cg07840143 0.1625 0.0372 1.24e-05 ++++ 0.1438508 1.0000000 chr5 3324860
56100 cg03544320 0.3008 0.0689 1.26e-05 -+++ 0.1438508 1.0000000 chr4 5894691 CRMP1 1stExon
330881 cg24053992 0.1754 0.0403 1.38e-05 +-++ 0.1468524 1.0000000 chr1 119554564
197997 cg13677022 -0.1546 0.0356 1.39e-05 —- 0.1468524 1.0000000 chr9 34625963 ARID3C Body
35348 cg02206980 -0.4156 0.0957 1.40e-05 —- 0.1468524 1.0000000 chr6 13574034 SIRT5;SIRT5 TSS1500;TSS1500
240943 cg16734734 0.1558 0.0360 1.52e-05 –++ 0.1545099 1.0000000 chr6 105624309 POPDC3;POPDC3 TSS200;5’UTR
64145 cg04080022 -0.1761 0.0409 1.66e-05 —+ 0.1646442 1.0000000 chr16 89648534 CPNE7;CPNE7 Body;Body
237459 cg16502049 -0.0984 0.0229 1.71e-05 —- 0.1648080 1.0000000 chr20 23402203 NAPB TSS200
218644 cg15025362 0.1569 0.0365 1.75e-05 ++-+ 0.1648080 1.0000000 chr3 186256331 CRYGS 3’UTR
113100 cg07399977 -0.1659 0.0387 1.82e-05 —- 0.1679212 1.0000000 chr1 27339612 FAM46B TSS1500
301289 cg21629895 -0.1761 0.0412 1.88e-05 —- 0.1679212 1.0000000 chr2 25565795 DNMT3A;DNMT3A;DNMT3A TSS1500;TSS1500;TSS1500
58832 cg03720762 -0.2458 0.0576 1.96e-05 —- 0.1679212 1.0000000 chr17 17604184 RAI1 5’UTR
168281 cg11414610 -0.1279 0.0300 1.96e-05 —- 0.1679212 1.0000000 chr19 16528319 EPS15L1 Body
176796 cg12065616 -0.1588 0.0373 2.03e-05 —- 0.1700595 1.0000000 chr12 94954828
6030 cg00358880 0.1679 0.0395 2.16e-05 ++++ 0.1768628 1.0000000 chr1 197885105 LHX9;LHX9 TSS1500;Body
191691 cg13278267 0.1750 0.0414 2.36e-05 ++++ 0.1847510 1.0000000 chr2 38742843
21418 cg01303372 -0.1905 0.0451 2.43e-05 —- 0.1847510 1.0000000 chr10 121415189 BAG3 Body
228619 cg15830431 0.1587 0.0376 2.43e-05 ++-+ 0.1847510 1.0000000 chr8 99952591
150668 cg10098010 0.2199 0.0521 2.45e-05 ++++ 0.1847510 1.0000000 chr6 138483709 KIAA1244 Body
34800 cg02166532 0.1646 0.0392 2.61e-05 ++++ 0.1883103 1.0000000 chr11 2159853 INS-IGF2;IGF2;IGF2;IGF2;IGF2 Body;Body;5’UTR;5’UTR;1stExon
91398 cg05926253 0.1388 0.0331 2.70e-05 -+++ 0.1883103 1.0000000 chr5 1801364 NDUFS6;MRPL36 TSS200;TSS1500
196894 cg13609065 0.0857 0.0204 2.72e-05 -+++ 0.1883103 1.0000000 chr17 6613894 SLC13A5;SLC13A5 Body;Body
356139 cg26090406 0.2617 0.0624 2.76e-05 ++++ 0.1883103 1.0000000 chr13 110937644 COL4A1 Body
50150 cg03149958 -0.1704 0.0408 2.91e-05 —- 0.1883103 1.0000000 chr6 36326677
5363 cg00321074 -0.1267 0.0303 2.92e-05 —- 0.1883103 1.0000000 chr3 19990693 RAB5A 5’UTR
331853 cg24127593 0.1811 0.0433 2.95e-05 ++++ 0.1883103 1.0000000 chr4 1648399 FAM53A Body
48278 cg03025061 -0.1653 0.0396 2.96e-05 —- 0.1883103 1.0000000 chr8 109261275 EIF3E TSS1500
33761 cg02097144 0.1717 0.0411 2.99e-05 +-++ 0.1883103 1.0000000 chr7 78280216 MAGI2 Body
117587 cg07712198 0.1970 0.0472 3.04e-05 -+++ 0.1883103 1.0000000 chr5 9015582
93 cg00004257 0.2233 0.0536 3.06e-05 ++++ 0.1883103 1.0000000 chr1 34629175 CSMD2 Body
180441 cg12354986 -0.1980 0.0475 3.09e-05 +— 0.1883103 1.0000000 chr22 38142174 TRIOBP;TRIOBP;TRIOBP TSS200;Body;TSS200
136896 cg09088406 0.2510 0.0603 3.17e-05 ++++ 0.1900531 1.0000000 chr15 27819306
323848 cg23504707 0.1527 0.0367 3.24e-05 ++++ 0.1904752 1.0000000 chr14 60712563 PPM1A;PPM1A 5’UTR;1stExon
80941 cg05197323 -0.1184 0.0285 3.28e-05 +— 0.1904752 1.0000000 chr14 24912098 SDR39U1 TSS200
351351 cg25687423 -0.1619 0.0391 3.47e-05 —- 0.1983951 1.0000000 chr6 43193521 C6orf108;C6orf108 Body;3’UTR
218811 cg15035705 -0.1756 0.0425 3.67e-05 —- 0.2050633 1.0000000 chr5 179159291 MAML1 TSS1500
166619 cg11289100 0.2128 0.0516 3.75e-05 ++++ 0.2050633 1.0000000 chr17 19313024 RNF112 TSS1500
325843 cg23662713 0.2955 0.0717 3.75e-05 ++++ 0.2050633 1.0000000 chr14 36741645
217427 cg14931071 0.1339 0.0325 3.80e-05 —+ 0.2050633 1.0000000 chr6 12717776 PHACTR1 TSS200
316250 cg22915154 -0.2026 0.0493 3.95e-05 —- 0.2100410 1.0000000 chr11 68816030 TPCN2 TSS1500
247434 cg17260318 -0.1813 0.0442 4.04e-05 —- 0.2118407 1.0000000 chr19 4067604 ZBTB7A TSS1500
86700 cg05595134 0.3324 0.0811 4.18e-05 +-++ 0.2140702 1.0000000 chr8 55047255 MRPL15 TSS1500
292390 cg20899625 -0.1360 0.0332 4.20e-05 —- 0.2140702 1.0000000 chr3 126721131 PLXNA1 Body
352336 cg25763542 -0.2870 0.0702 4.36e-05 —- 0.2160684 1.0000000 chr19 310512 MIER2 Body
20130 cg01218206 -0.1738 0.0426 4.44e-05 —+ 0.2160684 1.0000000 chr11 116933977 SIK3 Body
173650 cg11831006 -0.1901 0.0466 4.49e-05 —- 0.2160684 1.0000000 chr3 125100635
307701 cg22193385 -0.1780 0.0436 4.52e-05 –+- 0.2160684 1.0000000 chr12 52638005 KRT7 Body
304218 cg21885638 -0.1256 0.0308 4.53e-05 —- 0.2160684 1.0000000 chr3 129306552 PLXND1 Body
324549 cg23558842 0.2833 0.0695 4.59e-05 ++++ 0.2160684 1.0000000 chr11 15095178 CALCB;CALCB 1stExon;5’UTR
73455 cg04696969 0.2340 0.0574 4.64e-05 ++++ 0.2160684 1.0000000 chr2 223335429 SGPP2 Body
233115 cg16188243 -0.2292 0.0564 4.79e-05 —- 0.2192273 1.0000000 chr19 2783719 SGTA TSS1500
30412 cg01892516 0.4813 0.1184 4.82e-05 ++++ 0.2192273 1.0000000 chr14 38064532 FOXA1 TSS200
168526 cg11434671 -0.1410 0.0347 4.92e-05 —- 0.2198846 1.0000000 chr17 74524611 CYGB 3’UTR
222274 cg15323873 -0.1523 0.0375 4.95e-05 —- 0.2198846 1.0000000 chr10 79650526 DLG5 Body
168429 cg11425470 -0.1704 0.0420 5.06e-05 —- 0.2221106 1.0000000 chr1 109271795 FNDC7 Body
17916 cg01078824 0.1416 0.0350 5.13e-05 ++++ 0.2224636 1.0000000 chr7 27220047 HOXA10 TSS200
219413 cg15083775 0.1294 0.0320 5.25e-05 –++ 0.2244178 1.0000000 chr17 48054048
228483 cg15822394 -0.1875 0.0464 5.29e-05 —- 0.2244178 1.0000000 chr19 17877733 FCHO1;FCHO1;FCHO1;FCHO1 Body;Body;Body;Body
162133 cg10945313 0.1774 0.0440 5.50e-05 ++++ 0.2306034 1.0000000 chr4 113739291 ANK2;ANK2 5’UTR;1stExon
223845 cg15454856 0.0991 0.0246 5.76e-05 ++-+ 0.2389337 1.0000000 chr7 108168130 PNPLA8 TSS1500
225048 cg15557168 0.4852 0.1208 5.90e-05 +-++ 0.2414276 1.0000000 chr22 42548783
275492 cg19519624 -0.2199 0.0548 5.96e-05 —- 0.2414276 1.0000000 chr9 138881792
192044 cg13305951 -0.2022 0.0504 6.10e-05 —- 0.2414276 1.0000000 chr17 19314618 RNF112;RNF112 1stExon;5’UTR
330819 cg24049616 0.1591 0.0397 6.22e-05 ++++ 0.2414276 1.0000000 chr16 55359029 IRX6 1stExon
358903 cg26290114 -0.1633 0.0408 6.22e-05 —- 0.2414276 1.0000000 chr13 52159332 WDFY2 Body
174808 cg11914514 -0.1747 0.0437 6.27e-05 —- 0.2414276 1.0000000 chr9 131218865 ODF2;ODF2 TSS1500;5’UTR
279041 cg19784205 -0.2088 0.0522 6.27e-05 —- 0.2414276 1.0000000 chr12 132473879 EP400 Body
34418 cg02141929 -0.1944 0.0486 6.38e-05 —- 0.2432580 1.0000000 chr16 56681544
134866 cg08928966 0.1305 0.0327 6.58e-05 +-++ 0.2459133 1.0000000 chr3 51859710

Top 100 GO terms

X ONTOLOGY TERM N DE P.DE FDR
GO:0010800 BP positive regulation of peptidyl-threonine phosphorylation 28 2 0.0012414 1
GO:0033135 BP regulation of peptidyl-serine phosphorylation 125 3 0.0014291 1
GO:0030507 MF spectrin binding 28 2 0.0023516 1
GO:0010494 CC cytoplasmic stress granule 69 2 0.0031785 1
GO:0010799 BP regulation of peptidyl-threonine phosphorylation 46 2 0.0034741 1
GO:0005000 MF vasopressin receptor activity 6 1 0.0035990 1
GO:0032535 BP regulation of cellular component size 359 4 0.0037773 1
GO:0009258 BP 10-formyltetrahydrofolate catabolic process 2 1 0.0039096 1
GO:0016155 MF formyltetrahydrofolate dehydrogenase activity 2 1 0.0039096 1
GO:0009397 BP folic acid-containing compound catabolic process 3 1 0.0042694 1
GO:0042560 BP pteridine-containing compound catabolic process 3 1 0.0042694 1
GO:0008361 BP regulation of cell size 169 3 0.0050394 1
GO:0005115 MF receptor tyrosine kinase-like orphan receptor binding 1 1 0.0052303 1
GO:0036517 BP chemoattraction of serotonergic neuron axon 1 1 0.0052303 1
GO:0060599 BP lateral sprouting involved in mammary gland duct morphogenesis 1 1 0.0052303 1
GO:0061347 BP planar cell polarity pathway involved in outflow tract morphogenesis 1 1 0.0052303 1
GO:0061348 BP planar cell polarity pathway involved in ventricular septum morphogenesis 1 1 0.0052303 1
GO:0061349 BP planar cell polarity pathway involved in cardiac right atrium morphogenesis 1 1 0.0052303 1
GO:0061350 BP planar cell polarity pathway involved in cardiac muscle tissue morphogenesis 1 1 0.0052303 1
GO:0061354 BP planar cell polarity pathway involved in pericardium morphogenesis 1 1 0.0052303 1
GO:1904934 BP negative regulation of cell proliferation in midbrain 1 1 0.0052303 1
GO:1904955 BP planar cell polarity pathway involved in midbrain dopaminergic neuron differentiation 1 1 0.0052303 1
GO:0048850 BP hypophysis morphogenesis 2 1 0.0056017 1
GO:1905438 BP non-canonical Wnt signaling pathway involved in midbrain dopaminergic neuron differentiation 2 1 0.0057409 1
GO:0036518 BP chemorepulsion of dopaminergic neuron axon 2 1 0.0058494 1
GO:0051885 BP positive regulation of timing of anagen 2 1 0.0058573 1
GO:0097325 BP melanocyte proliferation 3 1 0.0059866 1
GO:0042695 BP thelarche 3 1 0.0060342 1
GO:0060744 BP mammary gland branching involved in thelarche 3 1 0.0060342 1
GO:0060809 BP mesodermal to mesenchymal transition involved in gastrulation 2 1 0.0060434 1
GO:0060031 BP mediolateral intercalation 2 1 0.0063463 1
GO:0060775 BP planar cell polarity pathway involved in gastrula mediolateral intercalation 2 1 0.0063463 1
GO:0060002 MF plus-end directed microfilament motor activity 3 1 0.0066603 1
GO:1902435 BP regulation of male mating behavior 2 1 0.0066640 1
GO:1902437 BP positive regulation of male mating behavior 2 1 0.0066640 1
GO:1904933 BP regulation of cell proliferation in midbrain 2 1 0.0073534 1
GO:0042640 BP anagen 5 1 0.0074701 1
GO:0051884 BP regulation of timing of anagen 5 1 0.0074701 1
GO:0046543 BP development of secondary female sexual characteristics 5 1 0.0075654 1
GO:0061341 BP non-canonical Wnt signaling pathway involved in heart development 2 1 0.0077345 1
GO:0061346 BP planar cell polarity pathway involved in heart morphogenesis 2 1 0.0077345 1
GO:0090081 BP regulation of heart induction by regulation of canonical Wnt signaling pathway 4 1 0.0077679 1
GO:0090082 BP positive regulation of heart induction by negative regulation of canonical Wnt signaling pathway 4 1 0.0077679 1
GO:0016742 MF hydroxymethyl-, formyl- and related transferase activity 8 1 0.0078801 1
GO:0031594 CC neuromuscular junction 74 2 0.0082890 1
GO:2000243 BP positive regulation of reproductive process 77 2 0.0083074 1
GO:0045136 BP development of secondary sexual characteristics 7 1 0.0083250 1
GO:0048022 BP negative regulation of melanin biosynthetic process 4 1 0.0086266 1
GO:1900377 BP negative regulation of secondary metabolite biosynthetic process 4 1 0.0086266 1
GO:0090066 BP regulation of anatomical structure size 491 4 0.0090906 1
GO:0060762 BP regulation of branching involved in mammary gland duct morphogenesis 4 1 0.0091396 1
GO:0060067 BP cervix development 2 1 0.0093337 1
GO:0003308 BP negative regulation of Wnt signaling pathway involved in heart development 7 1 0.0094248 1
GO:0003408 BP optic cup formation involved in camera-type eye development 3 1 0.0098302 1
GO:0003138 BP primary heart field specification 3 1 0.0099138 1
GO:0060157 BP urinary bladder development 4 1 0.0101397 1
GO:0009256 BP 10-formyltetrahydrofolate metabolic process 5 1 0.0101432 1
GO:1902379 MF chemoattractant activity involved in axon guidance 2 1 0.0101929 1
GO:0021953 BP central nervous system neuron differentiation 186 3 0.0102959 1
GO:0001025 MF RNA polymerase III general transcription initiation factor binding 3 1 0.0103155 1
GO:0001156 MF TFIIIC-class transcription factor complex binding 3 1 0.0103155 1
GO:0048818 BP positive regulation of hair follicle maturation 5 1 0.0103953 1
GO:0001002 MF RNA polymerase III type 1 promoter sequence-specific DNA binding 3 1 0.0103974 1
GO:0001003 MF RNA polymerase III type 2 promoter sequence-specific DNA binding 3 1 0.0103974 1
GO:0080084 MF 5S rDNA binding 3 1 0.0103974 1
GO:0003213 BP cardiac right atrium morphogenesis 2 1 0.0106682 1
GO:0048852 BP diencephalon morphogenesis 3 1 0.0108245 1
GO:0106006 MF cytoskeletal protein-membrane anchor activity 3 1 0.0109384 1
GO:0060750 BP epithelial cell proliferation involved in mammary gland duct elongation 3 1 0.0110411 1
GO:0060751 BP branch elongation involved in mammary gland duct branching 3 1 0.0110411 1
GO:0038031 BP non-canonical Wnt signaling pathway via JNK cascade 6 1 0.0113371 1
GO:0098732 BP macromolecule deacylation 101 2 0.0116357 1
GO:0070245 BP positive regulation of thymocyte apoptotic process 5 1 0.0118200 1
GO:0034983 BP peptidyl-lysine deacetylation 7 1 0.0118657 1
GO:0001938 BP positive regulation of endothelial cell proliferation 107 2 0.0118838 1
GO:0033138 BP positive regulation of peptidyl-serine phosphorylation 91 2 0.0120043 1
GO:0100012 BP regulation of heart induction by canonical Wnt signaling pathway 5 1 0.0121810 1
GO:0060029 BP convergent extension involved in organogenesis 6 1 0.0122571 1
GO:0061702 CC inflammasome complex 15 1 0.0127027 1
GO:0036515 BP serotonergic neuron axon guidance 4 1 0.0128115 1
GO:0097476 BP spinal cord motor neuron migration 4 1 0.0129507 1
GO:0015386 MF potassium:proton antiporter activity 9 1 0.0131411 1
GO:0045927 BP positive regulation of growth 250 3 0.0132418 1
GO:0036514 BP dopaminergic neuron axon guidance 5 1 0.0134260 1
GO:1904938 BP planar cell polarity pathway involved in axon guidance 5 1 0.0134260 1
GO:0018105 BP peptidyl-serine phosphorylation 282 3 0.0134792 1
GO:0015385 MF sodium:proton antiporter activity 10 1 0.0135356 1
GO:1901216 BP positive regulation of neuron death 91 2 0.0139154 1
GO:0071374 BP cellular response to parathyroid hormone stimulus 8 1 0.0139668 1
GO:0071233 BP cellular response to leucine 10 1 0.0141602 1
GO:0060340 BP positive regulation of type I interferon-mediated signaling pathway 13 1 0.0142616 1
GO:0038030 BP non-canonical Wnt signaling pathway via MAPK cascade 7 1 0.0143467 1
GO:0003307 BP regulation of Wnt signaling pathway involved in heart development 9 1 0.0144283 1
GO:0060090 MF molecular adaptor activity 302 3 0.0144754 1
GO:0002862 BP negative regulation of inflammatory response to antigenic stimulus 14 1 0.0148018 1
GO:0044851 BP hair cycle phase 9 1 0.0149027 1
GO:0048819 BP regulation of hair follicle maturation 9 1 0.0149027 1
GO:0005451 MF monovalent cation:proton antiporter activity 11 1 0.0152620 1
GO:0021954 BP central nervous system neuron development 78 2 0.0153361 1
GO:0071107 BP response to parathyroid hormone 10 1 0.0155003 1

DVPs

DVP datasets for common CpGs

# results adjusted for age, sex, smoking

fact850_DVP = read.table('/Users/annebozack/Documents/arsenic_meta/generic-metal/FACT_DVP_AsCategorical_adjAgeSm_850k_092520.txt', sep = "\t", header = T)
fact450_DVP = read.table('/Users/annebozack/Documents/arsenic_meta/generic-metal/FACT_DVP_AsCategorical_adjAgeSm_450k_092520.txt', sep = "\t", header = T)
chilePBMC_DVP = read.table('/Users/annebozack/Documents/arsenic_meta/Chile_PBMCs_DVPs_updated-results_2020-11-29/age-sex-smoking.txt', sep = "\t", header = T)
chileBuccal_DVP = read.table('/Users/annebozack/Documents/arsenic_meta/Chile_buccal_DVPs_updated-results_2020-11-29/age-sex-smoking.txt', sep = "\t", header = T)

fact850_DVP = fact850_DVP[fact850_DVP$cpg %in% allCpg,]
fact450_DVP = fact450_DVP[fact450_DVP$cpg %in% allCpg,]
chilePBMC_DVP = chilePBMC_DVP[chilePBMC_DVP$cpg %in% allCpg,]
chileBuccal_DVP = chileBuccal_DVP[chileBuccal_DVP$cpg %in% allCpg,]

write.table(fact850_DVP, file = "/Users/annebozack/Documents/arsenic_meta/generic-metal/FACT_DVP_AsCategorical_adjAgeSm_850k_120420_common.txt", sep = "\t", row.names = FALSE, col.names = TRUE)
write.table(fact450_DVP, file = "/Users/annebozack/Documents/arsenic_meta/generic-metal/FACT_DVP_AsCategorical_adjAgeSm_450k_120420_common.txt", sep = "\t", row.names = FALSE, col.names = TRUE)
write.table(chilePBMC_DVP, file = "/Users/annebozack/Documents/arsenic_meta/generic-metal/chile-pbmcs-age-sex-smoking_DVP_120420_common.txt", sep = "\t", row.names = FALSE, col.names = TRUE)
write.table(chileBuccal_DVP, file = "/Users/annebozack/Documents/arsenic_meta/generic-metal/chile-buccal-age-sex-smoking_DVP_120420_common.txt", sep = "\t", row.names = FALSE, col.names = TRUE)


# results adjusted for age, sex, smoking, cells

fact850cell_DVP = read.table('/Users/annebozack/Documents/arsenic_meta/generic-metal/FACT_DVP_AsCategorical_adjCellAgeSm_850k_092520.txt', sep = "\t", header = T)
fact450cell_DVP = read.table('/Users/annebozack/Documents/arsenic_meta/generic-metal/FACT_DVP_AsCategorical_adjCellAgeSm_450k_092520.txt', sep = "\t", header = T)
chilePBMCcell_DVP = read.table('/Users/annebozack/Documents/arsenic_meta/Chile_PBMCs_DVPs_updated-results_2020-11-29/cell-age-sex-smoking.txt', sep = "\t", header = T)
chileBuccalcell_DVP = read.table('/Users/annebozack/Documents/arsenic_meta/Chile_buccal_DVPs_updated-results_2020-11-29/cell-age-sex-smoking.txt', sep = "\t", header = T)

fact850cell_DVP = fact850cell_DVP[fact850cell_DVP$cpg %in% allCpg,]
fact450cell_DVP = fact450cell_DVP[fact450cell_DVP$cpg %in% allCpg,]
chilePBMCcell_DVP = chilePBMCcell_DVP[chilePBMCcell_DVP$cpg %in% allCpg,]
chileBuccalcell_DVP = chileBuccalcell_DVP[chileBuccalcell_DVP$cpg %in% allCpg,]

write.table(fact850cell_DVP, file = "/Users/annebozack/Documents/arsenic_meta/generic-metal/FACT_DVP_AsCategorical_adjCellAgeSm_850k_120420_common.txt", sep = "\t", row.names = FALSE, col.names = TRUE)
write.table(fact450cell_DVP, file = "/Users/annebozack/Documents/arsenic_meta/generic-metal/FACT_DVP_AsCategorical_adjCellAgeSm_450k_120420_common.txt", sep = "\t", row.names = FALSE, col.names = TRUE)
write.table(chilePBMCcell_DVP, file = "/Users/annebozack/Documents/arsenic_meta/generic-metal/chile-pbmcs-cell-age-sex-smoking_DVP_120420_common.txt", sep = "\t", row.names = FALSE, col.names = TRUE)
write.table(chileBuccalcell_DVP, file = "/Users/annebozack/Documents/arsenic_meta/generic-metal/chile-buccal-cell-age-sex-smoking_DVP_120420_common.txt", sep = "\t", row.names = FALSE, col.names = TRUE)

Run in METAL

cd /Users/annebozack/Documents/arsenic_meta/generic-metal

MARKER "cpg"
EFFECT "DiffLevene"
PVAL "P.Value"
STDERR "std_err"
SCHEME STDERR

# SCHEME STDERR command and weights effect size estimates using the inverse of the corresponding standard errors
    
# no cell type adjustment, blood only
PROCESS /Users/annebozack/Documents/arsenic_meta/generic-metal/FACT_DVP_AsCategorical_adjAgeSm_850k_120420_common.txt
PROCESS /Users/annebozack/Documents/arsenic_meta/generic-metal/FACT_DVP_AsCategorical_adjAgeSm_450k_120420_common.txt
PROCESS /Users/annebozack/Documents/arsenic_meta/generic-metal/chile-pbmcs-age-sex-smoking_DVP_120420_common.txt
OUTFILE /Users/annebozack/Documents/arsenic_meta/generic-metal/blood_no_cell_common_DVP_120420 .tbl

ANALYZE

# no cell type adjustment, all samples
PROCESS /Users/annebozack/Documents/arsenic_meta/generic-metal/FACT_DVP_AsCategorical_adjAgeSm_850k_120420_common.txt
PROCESS /Users/annebozack/Documents/arsenic_meta/generic-metal/FACT_DVP_AsCategorical_adjAgeSm_450k_120420_common.txt
PROCESS /Users/annebozack/Documents/arsenic_meta/generic-metal/chile-pbmcs-age-sex-smoking_DVP_120420_common.txt
PROCESS /Users/annebozack/Documents/arsenic_meta/generic-metal/chile-buccal-age-sex-smoking_DVP_120420_common.txt
OUTFILE /Users/annebozack/Documents/arsenic_meta/generic-metal/all_no_cell_common_DVP_120420 .tbl

ANALYZE

# cell type adjustment, blood only  
PROCESS /Users/annebozack/Documents/arsenic_meta/generic-metal/FACT_DVP_AsCategorical_adjCellAgeSm_850k_120420_common.txt
PROCESS /Users/annebozack/Documents/arsenic_meta/generic-metal/FACT_DVP_AsCategorical_adjCellAgeSm_450k_120420_common.txt
PROCESS /Users/annebozack/Documents/arsenic_meta/generic-metal/chile-pbmcs-cell-age-sex-smoking_DVP_120420_common.txt
OUTFILE /Users/annebozack/Documents/arsenic_meta/generic-metal/blood_cell_common_DVP_120420 .tbl

ANALYZE

# cell type adjustment, all samples
PROCESS /Users/annebozack/Documents/arsenic_meta/generic-metal/FACT_DVP_AsCategorical_adjCellAgeSm_850k_120420_common.txt
PROCESS /Users/annebozack/Documents/arsenic_meta/generic-metal/FACT_DVP_AsCategorical_adjCellAgeSm_450k_120420_common.txt
PROCESS /Users/annebozack/Documents/arsenic_meta/generic-metal/chile-pbmcs-cell-age-sex-smoking_DVP_120420_common.txt
PROCESS /Users/annebozack/Documents/arsenic_meta/generic-metal/chile-buccal-cell-age-sex-smoking_DVP_120420_common.txt
OUTFILE /Users/annebozack/Documents/arsenic_meta/generic-metal/all_cell_common_DVP_120420 .tbl

ANALYZE

Without cell type adjustment

Blood only

metal_blood_noCell_DVP = read.table('/Users/annebozack/Documents/arsenic_meta/generic-metal/blood_no_cell_common_DVP_1204201.tbl', sep = "\t")

metal_blood_noCell_DVP = metalProcess(metal_blood_noCell_DVP)

write.csv(metal_blood_noCell_DVP, '/Users/annebozack/Documents/arsenic_meta/generic-metal/DVP_blood_no_cell_common_120420.csv')


# Significant probes

# Nominal P-value
table(metal_blood_noCell_DVP$P.value < 0.05)
#  FALSE   TRUE 
# 350920  26431

# FDR
table(metal_blood_noCell_DVP$P.FDR < 0.05)
# FALSE   TRUE 
# 377326     25 

table(metal_blood_noCell_DVP$P.FDR < 0.1)
# FALSE   TRUE 
# 377306     45 

# Bonferroni
table(metal_blood_noCell_DVP$P.Bonf < 0.05)
# FALSE   TRUE 
# 377346     5 


# GO analysis, FDR < 0.1 probes

go_metal_blood_noCell_DVP = gometh(sig.cpg = metal_blood_noCell_DVP$Name[metal_blood_noCell_DVP$P.FDR < 0.1], all.cpg = metal_blood_noCell_DVP$Name, array.type = '450K', anno = annAll2)
go_metal_blood_noCell_DVP = go_metal_blood_noCell_DVP[order(go_metal_blood_noCell_DVP$P.DE),]

table(go_metal_blood_noCell_DVP$P.DE<0.05)
# FALSE  TRUE 
# 22453   130 

table(go_metal_blood_noCell_DVP$FDR<0.05)
# FALSE  
# 22583 

write.csv(go_metal_blood_noCell_DVP[go_metal_blood_noCell_DVP$P.DE<0.05,], '/Users/annebozack/Documents/arsenic_meta/generic-metal/GO_DVP_blood_noCell_common_120420.csv')


# KEGG analysis, FDR < 0.1 probes

kegg_metal_blood_noCell_DVP = gometh(sig.cpg = metal_blood_noCell_DVP$Name[metal_blood_noCell_DVP$P.FDR < 0.1], all.cpg = metal_blood_noCell_DVP$Name, array.type = '450K', collection = 'KEGG', anno = annAll2)
kegg_metal_blood_noCell_DVP = kegg_metal_blood_noCell_DVP[order(kegg_metal_blood_noCell_DVP$P.DE),]

table(kegg_metal_blood_noCell_DVP$P.DE<0.05)
# FALSE  TRUE 
#  335     5 

table(kegg_metal_blood_noCell_DVP$FDR<0.05)
# FALSE  
# 340

write.csv(kegg_metal_blood_noCell_DVP[kegg_metal_blood_noCell_DVP$P.DE<0.05,], '/Users/annebozack/Documents/arsenic_meta/generic-metal/KEGG_DVP_blood_noCell_common_120420.csv')


# Plotting

gg_qqplot(metal_blood_noCell_DVP$P.value)
quartz.save('qq_metal_blood_noCell_DVP_120420.png', type = "png", dpi = 300)

manhattan_meta(metal_blood_noCell_DVP, FDR=T)
quartz.save('manhattan_metal_blood_noCell_DVP_120420.png', type = "png", dpi = 300)

volcano_meta(metal_blood_noCell_DVP, FDR = TRUE)
quartz.save('volcano_metal_blood_noCell_DVP_120420.png', type = "png", dpi = 300)
knitr::include_graphics("/Users/annebozack/Documents/arsenic_meta/generic-metal/qq_metal_blood_noCell_DVP_120420.png")

knitr::include_graphics("/Users/annebozack/Documents/arsenic_meta/generic-metal/manhattan_metal_blood_noCell_DVP_120420.png")

knitr::include_graphics("/Users/annebozack/Documents/arsenic_meta/generic-metal/volcano_metal_blood_noCell_DVP_120420.png")

Top 100 probes

X Name Effect StdErr P.value Direction P.FDR P.Bonf chr pos UCSC_RefGene_Name UCSC_RefGene_Group
321132 cg23281729 0.9488 0.1212 0.00e+00 -++ 0.0000000 0.0000000 chr18 78005477 PARD6G TSS200
268961 cg18971529 0.3420 0.0614 0.00e+00 ++- 0.0037974 0.0094036 chr21 30391563 RWDD2B 1stExon
50934 cg03205258 0.5963 0.1076 0.00e+00 +++ 0.0037974 0.0113922 chr22 19929274 TXNRD2;COMT;COMT 1stExon;1stExon;5’UTR
10618 cg00629117 0.9092 0.1674 1.00e-07 +++ 0.0052395 0.0209581 chr16 1844932 IGFALS;IGFALS;IGFALS TSS200;TSS1500;TSS1500
309909 cg22387890 0.5327 0.0993 1.00e-07 +++ 0.0060852 0.0304258 chr7 6145595 USP42 5’UTR
163279 cg11032634 0.6573 0.1251 1.00e-07 +++ 0.0092765 0.0556593 chr22 19929254 TXNRD2;COMT 1stExon;TSS200
189046 cg13054212 0.1060 0.0204 2.00e-07 +++ 0.0095797 0.0791305 chr4 186356202 C4orf47 Body
282819 cg20074307 0.0884 0.0171 2.00e-07 +++ 0.0095797 0.0892812 chr14 55092491 SAMD4A;SAMD4A Body;Body
261543 cg18380742 0.1049 0.0203 2.00e-07 +++ 0.0095797 0.0915831 chr1 61674366 NFIA;NFIA;NFIA;NFIA Body;Body;Body;Body
32578 cg02026246 0.1680 0.0328 3.00e-07 +++ 0.0095797 0.1129412 chr11 22687589 GAS2 TSS1500
374163 cg27425262 0.7281 0.1422 3.00e-07 +++ 0.0095797 0.1152807 chr2 113953981 PSD4;LOC440839 Body;Body
145256 cg09692492 -0.3016 0.0590 3.00e-07 0.0095797 0.1192052 chr22 23744717 ZDHHC8P Body
199880 cg13797228 0.1148 0.0225 3.00e-07 +++ 0.0095797 0.1270541 chr3 126076243 KLF15 TSS200
237588 cg16511076 0.1132 0.0223 4.00e-07 +++ 0.0095797 0.1435821 chr4 48887480 OCIAD2;OCIAD2 3’UTR;3’UTR
171628 cg11691429 0.1834 0.0361 4.00e-07 +++ 0.0095797 0.1436953 chr2 947634 SNTG2 Body
149284 cg09996597 0.4748 0.0945 5.00e-07 +++ 0.0118134 0.1890151 chr16 1844927 IGFALS;IGFALS;IGFALS TSS200;TSS1500;TSS1500
2783 cg00156336 -0.1921 0.0384 5.00e-07 0.0121840 0.2071280 chr2 75788423 FAM176A;FAM176A 5’UTR;TSS1500
124685 cg08207566 0.1099 0.0224 1.00e-06 +++ 0.0205510 0.3699172 chr4 174086461
93087 cg06039392 0.1376 0.0282 1.00e-06 +++ 0.0205954 0.3913130 chr4 187476953 MTNR1A TSS1500
41466 cg02593924 0.2792 0.0583 1.70e-06 +++ 0.0318107 0.6362138 chr16 1844998 IGFALS;IGFALS;IGFALS TSS200;TSS1500;TSS1500
313664 cg22712983 -0.2209 0.0464 1.90e-06 –+ 0.0332583 0.7139481 chr2 219187374 PNKD;PNKD TSS1500;Body
325001 cg23602489 0.1012 0.0213 1.90e-06 +++ 0.0332583 0.7316836 chr7 101508949 CUX1;CUX1;CUX1 Body;Body;Body
121859 cg08015590 -0.4238 0.0896 2.30e-06 0.0372265 0.8562094 chr7 2281924 NUDT1;NUDT1;NUDT1;NUDT1;NUDT1;NUDT1;FTSJ2;NUDT1;NUDT1;NUDT1 5’UTR;5’UTR;1stExon;TSS1500;5’UTR;5’UTR;TSS200;1stExon;5’UTR;TSS1500
135062 cg08942080 0.1515 0.0321 2.40e-06 +++ 0.0383483 0.9203591 chr12 124821568 NCOR2;NCOR2 Body;Body
169144 cg11494866 0.1017 0.0218 3.10e-06 +++ 0.0463085 1.0000000 chr8 42695070 THAP1;THAP1 Body;Body
516 cg00026731 -0.1223 0.0264 3.60e-06 0.0521470 1.0000000 chr18 55254092 FECH;FECH TSS200;TSS200
190991 cg13221086 0.1023 0.0223 4.30e-06 +++ 0.0595935 1.0000000 chr3 31809318 OSBPL10 Body
293675 cg21004290 0.1140 0.0249 4.50e-06 +++ 0.0611578 1.0000000 chr8 131250320 ASAP1 Body
301219 cg21623748 0.0943 0.0206 4.80e-06 +++ 0.0625101 1.0000000 chr12 54378787 HOXC10 TSS200
9019 cg00534624 0.2751 0.0604 5.20e-06 +++ 0.0632577 1.0000000 chr16 1845096 IGFALS;IGFALS;IGFALS TSS200;TSS1500;TSS1500
194801 cg13483984 0.1164 0.0256 5.50e-06 +++ 0.0632577 1.0000000 chr1 224580455 WDR26;WDR26 Body;Body
268251 cg18907098 0.0733 0.0161 5.50e-06 +++ 0.0632577 1.0000000 chr4 512994 PIGG;PIGG Body;Body
168599 cg11440940 0.0987 0.0217 5.50e-06 +++ 0.0632577 1.0000000 chr19 8510764 HNRNPM;HNRNPM Body;Body
259345 cg18206914 0.0839 0.0185 5.80e-06 +++ 0.0640024 1.0000000 chr22 50963825 SCO2;SCO2;SCO2;SCO2 5’UTR;5’UTR;5’UTR;5’UTR
156274 cg10502904 0.1611 0.0356 6.10e-06 +++ 0.0640024 1.0000000 chr10 131565289 MGMT 3’UTR
132616 cg08770961 0.2938 0.0651 6.30e-06 +++ 0.0640024 1.0000000 chr16 66956122 RRAD;RRAD Body;Body
59640 cg03770962 0.1059 0.0235 6.40e-06 +++ 0.0640024 1.0000000 chr7 148477754 CUL1 Body
64658 cg04111999 0.0991 0.0220 6.50e-06 +++ 0.0640024 1.0000000 chr10 22615540 BMI1 Body
335850 cg24454243 -0.2036 0.0452 6.70e-06 0.0640024 1.0000000 chr7 105221985 EFCAB10 TSS200
229928 cg15931233 0.0956 0.0212 6.80e-06 +++ 0.0640024 1.0000000 chr5 53455496 ARL15 Body
80568 cg05169951 0.1850 0.0411 7.00e-06 +++ 0.0640024 1.0000000 chr16 3017955 KREMEN2;PAQR4;KREMEN2 Body;TSS1500;Body
178342 cg12175949 0.3443 0.0769 7.60e-06 +++ 0.0679591 1.0000000 chr22 19929286 TXNRD2;COMT;COMT 1stExon;1stExon;5’UTR
259615 cg18228116 0.3258 0.0735 9.30e-06 -++ 0.0820168 1.0000000 chr10 133995345 JAKMIP3 3’UTR
349119 cg25499746 0.0792 0.0179 9.90e-06 +++ 0.0845695 1.0000000 chr6 16346054 ATXN1;ATXN1 5’UTR;5’UTR
48009 cg03004999 -0.0816 0.0186 1.15e-05 0.0960149 1.0000000 chr7 43152125 HECW1 TSS200
26185 cg01614020 0.2522 0.0577 1.24e-05 +++ 0.1014746 1.0000000 chr8 24814137 NEFL TSS200
240531 cg16707423 0.0797 0.0183 1.29e-05 +++ 0.1016671 1.0000000 chr1 227167020 CABC1 Body
38724 cg02415779 0.1130 0.0259 1.32e-05 -++ 0.1016671 1.0000000 chr22 18527778
323330 cg23463533 0.0930 0.0214 1.33e-05 +++ 0.1016671 1.0000000 chr7 154473289 DPP6;DPP6;DPP6 Body;Body;Body
129911 cg08575722 -0.1195 0.0275 1.36e-05 0.1016671 1.0000000 chr11 32421845 WT1;WT1;WT1;WT1 Body;Body;Body;Body
70352 cg04485956 0.2005 0.0461 1.38e-05 +++ 0.1016671 1.0000000 chr2 1859071 MYT1L Body
80361 cg05157266 0.1358 0.0313 1.40e-05 +++ 0.1016671 1.0000000 chr2 183901614 NCKAP1;NCKAP1 Body;Body
320947 cg23268677 0.2705 0.0625 1.50e-05 +++ 0.1051691 1.0000000 chr22 19929097 TXNRD2;COMT Body;TSS200
353609 cg25880954 0.7380 0.1705 1.50e-05 +++ 0.1051691 1.0000000 chr1 47900630 MGC12982;FOXD2 TSS1500;TSS1500
297153 cg21270743 0.0928 0.0215 1.61e-05 +++ 0.1061227 1.0000000 chr1 156475001
191701 cg13279009 0.0804 0.0187 1.63e-05 -++ 0.1061227 1.0000000 chr2 24584023 ITSN2;ITSN2;ITSN2 TSS1500;TSS1500;TSS1500
305009 cg21951425 -0.1330 0.0309 1.63e-05 0.1061227 1.0000000 chr15 26108612 ATP10A TSS1500
291461 cg20805880 0.1028 0.0239 1.68e-05 +++ 0.1061227 1.0000000 chr15 73367293 NEO1 Body
332989 cg24215973 0.2223 0.0517 1.73e-05 +++ 0.1061227 1.0000000 chr2 240111563 HDAC4 Body
282764 cg20070659 0.2554 0.0595 1.76e-05 -++ 0.1061227 1.0000000 chr4 188736336
25526 cg01570086 -0.1220 0.0284 1.77e-05 0.1061227 1.0000000 chr15 74833080 ARID3B TSS1500
176205 cg12024822 0.1823 0.0425 1.81e-05 +++ 0.1061227 1.0000000 chr6 90597394
193732 cg13423098 0.1394 0.0325 1.81e-05 +++ 0.1061227 1.0000000 chr15 23807234
11224 cg00668103 0.1128 0.0263 1.82e-05 +++ 0.1061227 1.0000000 chr7 100084730 C7orf51 Body
196530 cg13587236 0.0904 0.0211 1.83e-05 +++ 0.1061227 1.0000000 chr9 128472496
361112 cg26453295 0.0812 0.0190 1.94e-05 +++ 0.1093224 1.0000000 chr19 54851740 LILRA4 TSS1500
329980 cg23990236 0.1245 0.0292 1.96e-05 -++ 0.1093224 1.0000000 chr1 12220146
223604 cg15439717 0.1095 0.0257 1.98e-05 +++ 0.1093224 1.0000000 chr13 23993016 SACS 5’UTR
309271 cg22336633 -0.1142 0.0268 2.00e-05 0.1093224 1.0000000 chr11 17099688 RPS13 TSS1500
127440 cg08400962 0.1029 0.0242 2.04e-05 +++ 0.1094849 1.0000000 chr19 34112316 CHST8;CHST8 TSS1500;TSS1500
299250 cg21476203 0.1083 0.0254 2.06e-05 +++ 0.1094849 1.0000000 chr8 144874281 SCRIB;SCRIB Body;Body
39898 cg02492873 0.1056 0.0248 2.14e-05 ++- 0.1111146 1.0000000 chr2 25193821 DNAJC27 Body
110491 cg07219314 -0.1568 0.0369 2.17e-05 0.1111146 1.0000000 chr22 23744725 ZDHHC8P Body
153889 cg10322744 0.4290 0.1011 2.18e-05 +++ 0.1111146 1.0000000 chr12 98910138 TMPO;TMPO;TMPO;LOC100128191 Body;Body;Body;TSS200
203197 cg14002714 0.1309 0.0310 2.37e-05 -++ 0.1192429 1.0000000 chr14 56095810 KTN1;KTN1;KTN1;KTN1 Body;Body;Body;Body
110227 cg07202461 0.0845 0.0201 2.53e-05 +++ 0.1257671 1.0000000 chr18 19406765 MIB1;MIR133A1 Body;TSS1500
50532 cg03176729 0.3304 0.0785 2.59e-05 +++ 0.1269762 1.0000000 chr10 124222607 HTRA1 Body
193559 cg13411311 -0.0913 0.0217 2.66e-05 0.1277739 1.0000000 chr2 241095989
157333 cg10577216 -0.1585 0.0377 2.68e-05 0.1277739 1.0000000 chr6 143265045 HIVEP2 5’UTR
111485 cg07290190 0.0927 0.0221 2.85e-05 ++- 0.1313439 1.0000000 chr4 121992756 C4orf31 5’UTR
59636 cg03770787 -0.2358 0.0564 2.87e-05 0.1313439 1.0000000 chr15 65652019 IGDCC3 Body
96749 cg06319359 0.0756 0.0181 2.88e-05 +++ 0.1313439 1.0000000 chr1 22109595 USP48;USP48;USP48;USP48 5’UTR;5’UTR;1stExon;1stExon
364539 cg26706070 0.0913 0.0218 2.89e-05 +++ 0.1313439 1.0000000 chr16 31119936 BCKDK;BCKDK 5’UTR;5’UTR
185794 cg12778178 0.1033 0.0247 2.93e-05 +++ 0.1313439 1.0000000 chr20 62583555 UCKL1AS;UCKL1 TSS1500;Body
147224 cg09845489 0.2355 0.0564 3.00e-05 +++ 0.1313439 1.0000000 chr7 157667853 PTPRN2;PTPRN2;PTPRN2 Body;Body;Body
259108 cg18190030 -0.1190 0.0285 3.03e-05 +– 0.1313439 1.0000000 chr1 234348636 SLC35F3 Body
58766 cg03717570 0.1286 0.0308 3.04e-05 +++ 0.1313439 1.0000000 chr17 73316496 GRB2;GRB2 Body;Body
155786 cg10468535 0.1263 0.0303 3.06e-05 +++ 0.1313439 1.0000000 chr7 157792053 PTPRN2;PTPRN2;PTPRN2 Body;Body;Body
125889 cg08285768 0.0863 0.0208 3.29e-05 +++ 0.1354434 1.0000000 chr15 86038622 AKAP13;AKAP13 Body;Body
116632 cg07642445 0.0668 0.0161 3.30e-05 +++ 0.1354434 1.0000000 chr6 27855795
261990 cg18414754 0.1826 0.0440 3.32e-05 +++ 0.1354434 1.0000000 chr3 138668832 C3orf72 Body
235393 cg16353272 0.0827 0.0199 3.34e-05 +++ 0.1354434 1.0000000 chr16 2124240 TSC2;TSC2;TSC2 Body;Body;Body
295936 cg21185289 0.2892 0.0698 3.38e-05 +++ 0.1354434 1.0000000 chr2 74743437 TLX2 3’UTR
351214 cg25674826 0.2435 0.0587 3.38e-05 +++ 0.1354434 1.0000000 chr21 35446543 MRPS6;SLC5A3 Body;5’UTR
253963 cg17805202 0.1087 0.0262 3.45e-05 +++ 0.1354434 1.0000000 chr1 239937440 CHRM3 5’UTR
90239 cg05850971 0.0924 0.0223 3.53e-05 +++ 0.1354434 1.0000000 chr6 32135027 EGFL8 Body
12204 cg00729699 -0.0914 0.0221 3.58e-05 0.1354434 1.0000000 chr8 21918075 EPB49;EPB49;EPB49;EPB49;EPB49;EPB49 5’UTR;5’UTR;5’UTR;5’UTR;5’UTR;5’UTR
363304 cg26618618 0.0956 0.0231 3.58e-05 +++ 0.1354434 1.0000000 chr11 95661178
355638 cg26051433 0.0958 0.0232 3.61e-05 +++ 0.1354434 1.0000000 chr10 75001410 FAM149B1 3’UTR
11047 cg00657529 0.0832 0.0201 3.61e-05 +++ 0.1354434 1.0000000 chr6 31698687 CLIC1;DDAH2 Body;TSS1500

Top 100 GO terms

X ONTOLOGY TERM N DE P.DE FDR
GO:0004325 MF ferrochelatase activity 1 1 0.0015112 1
GO:0042053 BP regulation of dopamine metabolic process 17 2 0.0018929 1
GO:0042069 BP regulation of catecholamine metabolic process 17 2 0.0018929 1
GO:0015036 MF disulfide oxidoreductase activity 39 2 0.0027763 1
GO:0070541 BP response to platinum ion 3 1 0.0039000 1
GO:0016363 CC nuclear matrix 103 3 0.0039500 1
GO:2000815 BP regulation of mRNA stability involved in response to oxidative stress 2 1 0.0041977 1
GO:0031337 BP positive regulation of sulfur amino acid metabolic process 1 1 0.0061113 1
GO:0050668 BP positive regulation of homocysteine metabolic process 1 1 0.0061113 1
GO:0042417 BP dopamine metabolic process 33 2 0.0061305 1
GO:0016667 MF oxidoreductase activity, acting on a sulfur group of donors 57 2 0.0063848 1
GO:0034399 CC nuclear periphery 124 3 0.0065066 1
GO:0051267 MF CP2 mannose-ethanolamine phosphotransferase activity 1 1 0.0065613 1
GO:0003908 MF methylated-DNA-[protein]-cysteine S-methyltransferase activity 1 1 0.0074068 1
GO:0050666 BP regulation of homocysteine metabolic process 2 1 0.0075457 1
GO:0001544 BP initiation of primordial ovarian follicle growth 2 1 0.0083648 1
GO:0000301 BP retrograde transport, vesicle recycling within Golgi 2 1 0.0085027 1
GO:0004416 MF hydroxyacylglutathione hydrolase activity 2 1 0.0087442 1
GO:0019243 BP methylglyoxal catabolic process to D-lactate via S-lactoyl-glutathione 2 1 0.0087442 1
GO:0051377 MF mannose-ethanolamine phosphotransferase activity 4 1 0.0090417 1
GO:0008502 MF melatonin receptor activity 3 1 0.0090824 1
GO:0045764 BP positive regulation of cellular amino acid metabolic process 3 1 0.0091048 1
GO:0016206 MF catechol O-methyltransferase activity 2 1 0.0092874 1
GO:0102084 MF L-dopa O-methyltransferase activity 2 1 0.0092874 1
GO:0102938 MF orcinol O-methyltransferase activity 2 1 0.0092874 1
GO:0006584 BP catecholamine metabolic process 46 2 0.0094643 1
GO:0009712 BP catechol-containing compound metabolic process 46 2 0.0094643 1
GO:0016036 BP cellular response to phosphate starvation 2 1 0.0096037 1
GO:0031335 BP regulation of sulfur amino acid metabolic process 3 1 0.0096910 1
GO:0051596 BP methylglyoxal catabolic process 3 1 0.0106621 1
GO:0061727 BP methylglyoxal catabolic process to lactate 3 1 0.0106621 1
GO:0005759 CC mitochondrial matrix 452 4 0.0107974 1
GO:0010610 BP regulation of mRNA stability involved in response to stress 3 1 0.0109776 1
GO:0035814 BP negative regulation of renal sodium excretion 3 1 0.0110177 1
GO:0001786 MF phosphatidylserine binding 56 2 0.0116723 1
GO:1901842 BP negative regulation of high voltage-gated calcium channel activity 4 1 0.0119888 1
GO:0042382 CC paraspeckles 6 1 0.0126671 1
GO:0051176 BP positive regulation of sulfur metabolic process 3 1 0.0130321 1
GO:0042698 BP ovulation cycle 69 2 0.0133490 1
GO:0009438 BP methylglyoxal metabolic process 5 1 0.0142031 1
GO:0008172 MF S-methyltransferase activity 6 1 0.0142529 1
GO:0006513 BP protein monoubiquitination 66 2 0.0142928 1
GO:0045914 BP negative regulation of catecholamine metabolic process 3 1 0.0143262 1
GO:0045963 BP negative regulation of dopamine metabolic process 3 1 0.0143262 1
GO:0016013 CC syntrophin complex 3 1 0.0147056 1
GO:0033238 BP regulation of cellular amine metabolic process 78 2 0.0147491 1
GO:0046501 BP protoporphyrinogen IX metabolic process 10 1 0.0156773 1
GO:0042420 BP dopamine catabolic process 5 1 0.0160319 1
GO:1903527 BP positive regulation of membrane tubulation 4 1 0.0162069 1
GO:1990452 CC Parkin-FBXW7-Cul1 ubiquitin ligase complex 3 1 0.0162837 1
GO:0050773 BP regulation of dendrite development 141 3 0.0170721 1
GO:0042180 BP cellular ketone metabolic process 251 3 0.0178267 1
GO:0032413 BP negative regulation of ion transmembrane transporter activity 72 2 0.0182638 1
GO:0051597 BP response to methylmercury 7 1 0.0188400 1
GO:0071535 MF RING-like zinc finger domain binding 4 1 0.0190520 1
GO:0019614 BP catechol-containing compound catabolic process 6 1 0.0191770 1
GO:0042424 BP catecholamine catabolic process 6 1 0.0191770 1
GO:0042567 CC insulin-like growth factor ternary complex 4 1 0.0192472 1
GO:0042182 BP ketone catabolic process 12 1 0.0199094 1
GO:0016942 CC insulin-like growth factor binding protein complex 5 1 0.0201819 1
GO:0036454 CC growth factor complex 5 1 0.0201819 1
GO:0046916 BP cellular transition metal ion homeostasis 104 2 0.0202261 1
GO:0072341 MF modified amino acid binding 84 2 0.0204407 1
GO:0004791 MF thioredoxin-disulfide reductase activity 7 1 0.0208452 1
GO:0001547 BP antral ovarian follicle growth 8 1 0.0217342 1
GO:1903525 BP regulation of membrane tubulation 6 1 0.0219949 1
GO:0036353 BP histone H2A-K119 monoubiquitination 8 1 0.0220516 1
GO:0034046 MF poly(G) binding 7 1 0.0226594 1
GO:0009008 MF DNA-methyltransferase activity 6 1 0.0227584 1
GO:0006878 BP cellular copper ion homeostasis 12 1 0.0230298 1
GO:0032410 BP negative regulation of transporter activity 83 2 0.0231043 1
GO:0010265 BP SCF complex assembly 6 1 0.0236882 1
GO:0033239 BP negative regulation of cellular amine metabolic process 6 1 0.0243470 1
GO:0042405 CC nuclear inclusion body 12 1 0.0243529 1
GO:0046185 BP aldehyde catabolic process 12 1 0.0244393 1
GO:0016668 MF oxidoreductase activity, acting on a sulfur group of donors, NAD(P) as acceptor 11 1 0.0250461 1
GO:0033240 BP positive regulation of cellular amine metabolic process 7 1 0.0250550 1
GO:1904063 BP negative regulation of cation transmembrane transport 86 2 0.0250751 1
GO:0019336 BP phenol-containing compound catabolic process 9 1 0.0258713 1
GO:0000151 CC ubiquitin ligase complex 273 3 0.0259841 1
GO:0055070 BP copper ion homeostasis 14 1 0.0260912 1
GO:0051051 BP negative regulation of transport 456 4 0.0264663 1
GO:0007614 BP short-term memory 10 1 0.0266638 1
GO:0044106 BP cellular amine metabolic process 122 2 0.0269691 1
GO:0006825 BP copper ion transport 15 1 0.0270306 1
GO:0042135 BP neurotransmitter catabolic process 9 1 0.0279874 1
GO:0006307 BP DNA dealkylation involved in DNA repair 10 1 0.0282932 1
GO:0051537 MF 2 iron, 2 sulfur cluster binding 21 1 0.0287087 1
GO:0009308 BP amine metabolic process 131 2 0.0295977 1
GO:0071803 BP positive regulation of podosome assembly 10 1 0.0296441 1
GO:0042762 BP regulation of sulfur metabolic process 13 1 0.0299326 1
GO:0050667 BP homocysteine metabolic process 13 1 0.0314888 1
GO:0071014 CC post-mRNA release spliceosomal complex 13 1 0.0323889 1
GO:0033617 BP mitochondrial cytochrome c oxidase assembly 21 1 0.0324808 1
GO:0048609 BP multicellular organismal reproductive process 769 5 0.0325911 1
GO:0015035 MF protein disulfide oxidoreductase activity 21 1 0.0331027 1
GO:0016254 BP preassembly of GPI anchor in ER membrane 16 1 0.0331426 1
GO:0017085 BP response to insecticide 11 1 0.0333218 1
GO:0046929 BP negative regulation of neurotransmitter secretion 10 1 0.0333587 1
GO:0034766 BP negative regulation of ion transmembrane transport 97 2 0.0333662 1

Including buccal

metal_all_noCell_DVP = read.table('/Users/annebozack/Documents/arsenic_meta/generic-metal/all_no_cell_common_DVP_1204201.tbl', sep = "\t")

metal_all_noCell_DVP = metalProcess(metal_all_noCell_DVP)

write.csv(metal_all_noCell_DVP, '/Users/annebozack/Documents/arsenic_meta/generic-metal/DVP_all_no_cell_common_120420.csv')


# Significant probes

# Nominal P-value
table(metal_all_noCell_DVP$P.value < 0.05)
#  FALSE   TRUE 
# 352439  24912

# FDR
table(metal_all_noCell_DVP$P.FDR < 0.05)
# FALSE     TRUE
# 377331     20 

table(metal_all_noCell_DVP$P.FDR < 0.1)
# FALSE     TRUE
# 377310     41  

# Bonferroni
table(metal_all_noCell_DVP$P.Bonf < 0.05)
# FALSE     TRUE
# 377346      5  


# GO analysis, FDR < 0.1 probes

go_metal_all_noCell_DVP = gometh(sig.cpg = metal_all_noCell_DVP$Name[metal_all_noCell_DVP$P.FDR < 0.1], all.cpg = metal_all_noCell_DVP$Name, array.type = '450K', anno = annAll2)
go_metal_all_noCell_DVP = go_metal_all_noCell_DVP[order(go_metal_all_noCell_DVP$P.DE),]

table(go_metal_all_noCell_DVP$P.DE<0.05)
# FALSE  TRUE 
#  22387   196 

table(go_metal_all_noCell_DVP$FDR<0.05)
# FALSE 
# 22583 

write.csv(go_metal_all_noCell_DVP[go_metal_all_noCell_DVP$P.DE<0.05,], '/Users/annebozack/Documents/arsenic_meta/generic-metal/GO_DVP_all_noCell_common_120420.csv')


# KEGG analysis, FDR < 0.1 probes

kegg_metal_all_noCell_DVP = gometh(sig.cpg = metal_all_noCell_DVP$Name[metal_all_noCell_DVP$P.FDR < 0.1], all.cpg = metal_all_noCell_DVP$Name, array.type = '450K', collection = 'KEGG', anno = annAll2)
kegg_metal_all_noCell_DVP = kegg_metal_all_noCell_DVP[order(kegg_metal_all_noCell_DVP$P.DE),]

table(kegg_metal_all_noCell_DVP$P.DE<0.05)
# FALSE  TRUE 
#  336     4  

table(kegg_metal_all_noCell_DVP$FDR<0.05)
# FALSE 
# 340 

write.csv(kegg_metal_all_noCell_DVP[kegg_metal_all_noCell_DVP$P.DE<0.05,], '/Users/annebozack/Documents/arsenic_meta/generic-metal/KEGG_DVP_all_noCell_common_120420.csv')



# Plotting

gg_qqplot(metal_all_noCell_DVP$P.value)
quartz.save('qq_metal_all_noCell_DVP_120420.png', type = "png", dpi = 300)

manhattan_meta(metal_all_noCell_DVP, FDR=T)
quartz.save('manhattan_metal_all_noCell_DVP_120420.png', type = "png", dpi = 300)

volcano_meta(metal_all_noCell_DVP, FDR = TRUE)
quartz.save('volcano_metal_all_noCell_DVP_120420.png', type = "png", dpi = 300)
knitr::include_graphics("/Users/annebozack/Documents/arsenic_meta/generic-metal/qq_metal_all_noCell_DVP_120420.png")

knitr::include_graphics("/Users/annebozack/Documents/arsenic_meta/generic-metal/manhattan_metal_all_noCell_DVP_120420.png")

knitr::include_graphics("/Users/annebozack/Documents/arsenic_meta/generic-metal/volcano_metal_all_noCell_DVP_120420.png")

Top 100 probes

X Name Effect StdErr P.value Direction P.FDR P.Bonf chr pos UCSC_RefGene_Name UCSC_RefGene_Group
321132 cg23281729 0.9672 0.1110 0.00e+00 -+++ 0.0000000 0.0000000 chr18 78005477 PARD6G TSS200
374163 cg27425262 0.8329 0.1216 0.00e+00 ++++ 0.0000014 0.0000029 chr2 113953981 PSD4;LOC440839 Body;Body
50934 cg03205258 0.5864 0.0973 0.00e+00 ++++ 0.0002130 0.0006389 chr22 19929274 TXNRD2;COMT;COMT 1stExon;1stExon;5’UTR
163279 cg11032634 0.6070 0.1118 1.00e-07 ++++ 0.0053971 0.0215883 chr22 19929254 TXNRD2;COMT 1stExon;TSS200
189046 cg13054212 0.1029 0.0191 1.00e-07 ++++ 0.0054112 0.0270561 chr4 186356202 C4orf47 Body
309909 cg22387890 0.4666 0.0890 2.00e-07 ++++ 0.0099055 0.0594328 chr7 6145595 USP42 5’UTR
190387 cg13171197 0.1154 0.0225 3.00e-07 +-++ 0.0148622 0.1040357 chr7 90916020
268961 cg18971529 0.3009 0.0592 4.00e-07 ++– 0.0150148 0.1381105 chr21 30391563 RWDD2B 1stExon
76120 cg04873963 -0.1042 0.0205 4.00e-07 —- 0.0150148 0.1436575 chr16 2518322
516 cg00026731 -0.1294 0.0255 4.00e-07 —- 0.0150148 0.1501480 chr18 55254092 FECH;FECH TSS200;TSS200
193559 cg13411311 -0.0993 0.0197 4.00e-07 —- 0.0151489 0.1666382 chr2 241095989
169072 cg11488033 0.3422 0.0683 5.00e-07 -+++ 0.0168487 0.2021847 chr3 196705898
2783 cg00156336 -0.1763 0.0354 6.00e-07 —- 0.0181854 0.2364104 chr2 75788423 FAM176A;FAM176A 5’UTR;TSS1500
145256 cg09692492 -0.2570 0.0520 8.00e-07 —- 0.0207220 0.2901074 chr22 23744717 ZDHHC8P Body
261543 cg18380742 0.0983 0.0200 9.00e-07 +++- 0.0231769 0.3476535 chr1 61674366 NFIA;NFIA;NFIA;NFIA Body;Body;Body;Body
313664 cg22712983 -0.2239 0.0460 1.10e-06 –+- 0.0262259 0.4196143 chr2 219187374 PNKD;PNKD TSS1500;Body
237588 cg16511076 0.1075 0.0222 1.30e-06 +++- 0.0280572 0.4769717 chr4 48887480 OCIAD2;OCIAD2 3’UTR;3’UTR
282819 cg20074307 0.0791 0.0165 1.60e-06 +++- 0.0311503 0.5856488 chr14 55092491 SAMD4A;SAMD4A Body;Body
353609 cg25880954 0.7123 0.1485 1.60e-06 ++++ 0.0311503 0.6120633 chr1 47900630 MGC12982;FOXD2 TSS1500;TSS1500
291461 cg20805880 0.1020 0.0213 1.70e-06 ++++ 0.0311503 0.6230065 chr15 73367293 NEO1 Body
124685 cg08207566 0.1017 0.0218 3.00e-06 +++- 0.0544284 1.0000000 chr4 174086461
178342 cg12175949 0.2930 0.0631 3.40e-06 ++++ 0.0573409 1.0000000 chr22 19929286 TXNRD2;COMT;COMT 1stExon;1stExon;5’UTR
135062 cg08942080 0.1397 0.0301 3.50e-06 ++++ 0.0573409 1.0000000 chr12 124821568 NCOR2;NCOR2 Body;Body
219690 cg15104380 -0.0789 0.0170 3.70e-06 +— 0.0574026 1.0000000 chr10 99285205 UBTD1 Body
282709 cg20066496 -0.1821 0.0394 3.80e-06 —- 0.0574026 1.0000000 chr15 43213993 TTBK2 TSS1500
93087 cg06039392 0.1254 0.0272 4.10e-06 +++- 0.0584615 1.0000000 chr4 187476953 MTNR1A TSS1500
309271 cg22336633 -0.1142 0.0248 4.20e-06 —- 0.0584615 1.0000000 chr11 17099688 RPS13 TSS1500
64658 cg04111999 0.0980 0.0214 4.60e-06 ++++ 0.0616834 1.0000000 chr10 22615540 BMI1 Body
293675 cg21004290 0.1086 0.0238 5.00e-06 ++++ 0.0651906 1.0000000 chr8 131250320 ASAP1 Body
346588 cg25298319 -0.4235 0.0932 5.60e-06 —- 0.0688970 1.0000000 chr2 233217079
32578 cg02026246 0.1322 0.0291 5.70e-06 +++- 0.0688970 1.0000000 chr11 22687589 GAS2 TSS1500
339841 cg24754507 -0.0947 0.0209 5.90e-06 —- 0.0697038 1.0000000 chr6 28481862 GPX6 Body
268251 cg18907098 0.0729 0.0161 6.20e-06 +++- 0.0713994 1.0000000 chr4 512994 PIGG;PIGG Body;Body
171628 cg11691429 0.1555 0.0346 7.00e-06 +++- 0.0781339 1.0000000 chr2 947634 SNTG2 Body
92754 cg06013413 0.0904 0.0202 7.40e-06 -+++ 0.0795497 1.0000000 chr8 627560 ERICH1 Body
332456 cg24168538 0.2387 0.0534 7.80e-06 ++++ 0.0795497 1.0000000 chr4 35527016
342170 cg24933709 0.1027 0.0230 7.80e-06 ++++ 0.0795497 1.0000000 chr7 149120687
23625 cg01445793 0.1780 0.0400 8.70e-06 ++++ 0.0862942 1.0000000 chr17 3771578 CAMKK1;CAMKK1;CAMKK1 Body;Body;Body
129911 cg08575722 -0.1203 0.0272 1.01e-05 —- 0.0965075 1.0000000 chr11 32421845 WT1;WT1;WT1;WT1 Body;Body;Body;Body
361112 cg26453295 0.0817 0.0185 1.02e-05 ++++ 0.0965075 1.0000000 chr19 54851740 LILRA4 TSS1500
305009 cg21951425 -0.1306 0.0296 1.06e-05 —- 0.0976511 1.0000000 chr15 26108612 ATP10A TSS1500
9817 cg00581043 -0.2105 0.0480 1.15e-05 —- 0.1034285 1.0000000 chr6 168106129
173107 cg11797898 -0.1299 0.0297 1.19e-05 —- 0.1034285 1.0000000 chr7 1983375 MAD1L1;MAD1L1;MAD1L1 Body;Body;Body
323330 cg23463533 0.0904 0.0207 1.21e-05 ++++ 0.1034285 1.0000000 chr7 154473289 DPP6;DPP6;DPP6 Body;Body;Body
126025 cg08293531 -0.1206 0.0276 1.25e-05 —- 0.1038536 1.0000000 chr15 101601180 LRRK1 Body
48009 cg03004999 -0.0716 0.0164 1.27e-05 —- 0.1038536 1.0000000 chr7 43152125 HECW1 TSS200
80568 cg05169951 0.1712 0.0393 1.31e-05 ++++ 0.1051766 1.0000000 chr16 3017955 KREMEN2;PAQR4;KREMEN2 Body;TSS1500;Body
147224 cg09845489 0.2281 0.0527 1.48e-05 ++++ 0.1130573 1.0000000 chr7 157667853 PTPRN2;PTPRN2;PTPRN2 Body;Body;Body
156274 cg10502904 0.1329 0.0307 1.50e-05 ++++ 0.1130573 1.0000000 chr10 131565289 MGMT 3’UTR
90548 cg05872129 0.5015 0.1159 1.50e-05 ++++ 0.1130573 1.0000000 chr22 39784769
292637 cg20923605 0.2592 0.0599 1.53e-05 ++++ 0.1130573 1.0000000 chr13 112978683
265757 cg18716164 0.1169 0.0271 1.58e-05 ++++ 0.1145115 1.0000000 chr19 30019647 VSTM2B Body
335850 cg24454243 -0.1659 0.0385 1.61e-05 —- 0.1148125 1.0000000 chr7 105221985 EFCAB10 TSS200
38724 cg02415779 0.1107 0.0257 1.64e-05 -++- 0.1148125 1.0000000 chr22 18527778
349119 cg25499746 0.0767 0.0179 1.77e-05 +++- 0.1217128 1.0000000 chr6 16346054 ATXN1;ATXN1 5’UTR;5’UTR
219405 cg15083015 0.1789 0.0417 1.82e-05 ++++ 0.1226391 1.0000000 chr11 20625714 SLC6A5 Body
339775 cg24748746 -0.2074 0.0485 1.86e-05 —- 0.1232680 1.0000000 chr7 155738916
9019 cg00534624 0.2244 0.0525 1.94e-05 ++++ 0.1239502 1.0000000 chr16 1845096 IGFALS;IGFALS;IGFALS TSS200;TSS1500;TSS1500
91411 cg05926928 0.4655 0.1090 1.94e-05 ++++ 0.1239502 1.0000000 chr17 57297772 GDPD1;GDPD1;GDPD1 TSS200;TSS200;TSS200
95795 cg06239191 0.1902 0.0447 2.08e-05 ++++ 0.1256788 1.0000000 chr8 145163136 KIAA1875 Body
370181 cg27121095 0.1067 0.0251 2.09e-05 -+++ 0.1256788 1.0000000 chr18 77155145 NFATC1;NFATC1;NFATC1 TSS1500;TSS1500;TSS1500
194801 cg13483984 0.1031 0.0243 2.13e-05 +++- 0.1256788 1.0000000 chr1 224580455 WDR26;WDR26 Body;Body
153889 cg10322744 0.4052 0.0953 2.14e-05 ++++ 0.1256788 1.0000000 chr12 98910138 TMPO;TMPO;TMPO;LOC100128191 Body;Body;Body;TSS200
329980 cg23990236 0.1203 0.0283 2.16e-05 -+++ 0.1256788 1.0000000 chr1 12220146
259615 cg18228116 0.2965 0.0700 2.27e-05 -+++ 0.1256788 1.0000000 chr10 133995345 JAKMIP3 3’UTR
128672 cg08487455 0.1474 0.0348 2.29e-05 ++++ 0.1256788 1.0000000 chr16 76311050 CNTNAP4 TSS200
131033 cg08654960 -0.1347 0.0319 2.36e-05 —- 0.1256788 1.0000000 chr16 85319859
12204 cg00729699 -0.0920 0.0218 2.36e-05 —- 0.1256788 1.0000000 chr8 21918075 EPB49;EPB49;EPB49;EPB49;EPB49;EPB49 5’UTR;5’UTR;5’UTR;5’UTR;5’UTR;5’UTR
235393 cg16353272 0.0828 0.0196 2.36e-05 ++++ 0.1256788 1.0000000 chr16 2124240 TSC2;TSC2;TSC2 Body;Body;Body
91432 cg05927817 0.3361 0.0795 2.36e-05 ++++ 0.1256788 1.0000000 chr6 18020357
80361 cg05157266 0.1310 0.0310 2.38e-05 +++- 0.1256788 1.0000000 chr2 183901614 NCKAP1;NCKAP1 Body;Body
193732 cg13423098 0.1356 0.0321 2.40e-05 +++- 0.1256788 1.0000000 chr15 23807234
277830 cg19702802 0.1563 0.0370 2.46e-05 ++++ 0.1262596 1.0000000 chr19 46417729 NANOS2 1stExon
159378 cg10729167 0.1354 0.0321 2.48e-05 ++++ 0.1262596 1.0000000 chr10 111220101
337433 cg24577193 -0.3193 0.0759 2.57e-05 —- 0.1274285 1.0000000 chr1 78148396 ZZZ3 TSS200
269647 cg19029220 -0.0802 0.0191 2.61e-05 +— 0.1274285 1.0000000 chr2 64067822 UGP2;UGP2 TSS1500;TSS1500
321501 cg23313031 -0.0993 0.0236 2.63e-05 —- 0.1274285 1.0000000 chr6 29974745 HLA-J;NCRNA00171 Body;Body
320947 cg23268677 0.2321 0.0552 2.63e-05 ++++ 0.1274285 1.0000000 chr22 19929097 TXNRD2;COMT Body;TSS200
196530 cg13587236 0.0881 0.0210 2.71e-05 +++- 0.1294457 1.0000000 chr9 128472496
64158 cg04080724 0.1031 0.0246 2.82e-05 ++++ 0.1327804 1.0000000 chr4 140202327 C4orf49 TSS1500
162593 cg10980774 0.1419 0.0341 3.12e-05 ++++ 0.1450755 1.0000000 chr11 112832547 NCAM1;NCAM1;NCAM1 Body;Body;Body
4028 cg00238318 -0.1141 0.0274 3.18e-05 –+- 0.1450755 1.0000000 chr10 94607950 EXOC6;EXOC6 Body;TSS1500
39898 cg02492873 0.1026 0.0247 3.19e-05 ++– 0.1450755 1.0000000 chr2 25193821 DNAJC27 Body
348207 cg25423077 0.3801 0.0915 3.26e-05 ++++ 0.1463134 1.0000000 chr18 59221601 CDH20 Body
338787 cg24682751 -0.1872 0.0451 3.36e-05 —- 0.1488781 1.0000000 chr15 93591750 RGMA;RGMA;RGMA;RGMA;RGMA;RGMA Body;Body;Body;Body;Body;Body
190991 cg13221086 0.0873 0.0211 3.39e-05 +++- 0.1488781 1.0000000 chr3 31809318 OSBPL10 Body
95484 cg06216157 -0.0646 0.0156 3.47e-05 –+- 0.1506368 1.0000000 chr17 7210363 EIF5A;EIF5A;EIF5A;EIF5A;EIF5A TSS1500;5’UTR;TSS1500;TSS1500;1stExon
179110 cg12235073 0.1005 0.0243 3.57e-05 ++++ 0.1528272 1.0000000 chr10 6270423 PFKFB3;PFKFB3 Body;Body
167176 cg11332363 0.1782 0.0431 3.64e-05 ++-+ 0.1528272 1.0000000 chr19 54023999 ZNF331 TSS200
304836 cg21936789 0.1721 0.0417 3.64e-05 ++++ 0.1528272 1.0000000 chr3 47620545 CSPG5 TSS200
5926 cg00353112 -0.0979 0.0238 3.82e-05 —- 0.1570929 1.0000000 chr15 45879221 PLDN TSS200
69221 cg04406454 -0.1479 0.0359 3.83e-05 —- 0.1570929 1.0000000 chr6 10398494 TFAP2A;TFAP2A;TFAP2A 3’UTR;3’UTR;3’UTR
110491 cg07219314 -0.1410 0.0343 3.88e-05 —- 0.1573107 1.0000000 chr22 23744725 ZDHHC8P Body
295936 cg21185289 0.2772 0.0675 4.02e-05 ++++ 0.1613376 1.0000000 chr2 74743437 TLX2 3’UTR
107294 cg07019740 0.2793 0.0681 4.07e-05 ++++ 0.1616651 1.0000000 chr22 19929205 TXNRD2;COMT Body;TSS200
362881 cg26580480 -0.0960 0.0234 4.18e-05 —- 0.1643442 1.0000000 chr6 43241339 TTBK1 Body
229928 cg15931233 0.0783 0.0191 4.34e-05 ++++ 0.1680165 1.0000000 chr5 53455496 ARL15 Body
135334 cg08963616 0.0861 0.0211 4.37e-05 ++++ 0.1680165 1.0000000 chr8 17249585 MTMR7 Body
59640 cg03770962 0.0905 0.0221 4.41e-05 +++- 0.1680165 1.0000000 chr7 148477754 CUL1 Body
87925 cg05677467 0.0620 0.0152 4.50e-05 ++-+ 0.1698457 1.0000000 chr15 85197654 WDR73 TSS200

Top 100 GO terms

X ONTOLOGY TERM N DE P.DE FDR
GO:0034156 BP negative regulation of toll-like receptor 7 signaling pathway 1 1 0.0006729 1
GO:0004325 MF ferrochelatase activity 1 1 0.0008725 1
GO:0042053 BP regulation of dopamine metabolic process 18 2 0.0013589 1
GO:0042069 BP regulation of catecholamine metabolic process 18 2 0.0013589 1
GO:0048609 BP multicellular organismal reproductive process 753 6 0.0016644 1
GO:0032504 BP multicellular organism reproduction 768 6 0.0017622 1
GO:0032997 CC Fc receptor complex 3 1 0.0019011 1
GO:0032998 CC Fc-epsilon receptor I complex 3 1 0.0019011 1
GO:0034155 BP regulation of toll-like receptor 7 signaling pathway 3 1 0.0019833 1
GO:0042417 BP dopamine metabolic process 33 2 0.0038976 1
GO:0031337 BP positive regulation of sulfur amino acid metabolic process 1 1 0.0048329 1
GO:0050668 BP positive regulation of homocysteine metabolic process 1 1 0.0048329 1
GO:1904527 BP negative regulation of microtubule binding 2 1 0.0049443 1
GO:0050666 BP regulation of homocysteine metabolic process 2 1 0.0055603 1
GO:1902816 BP regulation of protein localization to microtubule 5 1 0.0055794 1
GO:1902817 BP negative regulation of protein localization to microtubule 5 1 0.0055794 1
GO:0051267 MF CP2 mannose-ethanolamine phosphotransferase activity 1 1 0.0057471 1
GO:0072299 BP negative regulation of metanephric glomerulus development 1 1 0.0058507 1
GO:0072302 BP negative regulation of metanephric glomerular mesangial cell proliferation 1 1 0.0058507 1
GO:0006584 BP catecholamine metabolic process 46 2 0.0058803 1
GO:0009712 BP catechol-containing compound metabolic process 46 2 0.0058803 1
GO:0008502 MF melatonin receptor activity 3 1 0.0059440 1
GO:0001544 BP initiation of primordial ovarian follicle growth 2 1 0.0062992 1
GO:0031335 BP regulation of sulfur amino acid metabolic process 3 1 0.0063248 1
GO:0016036 BP cellular response to phosphate starvation 2 1 0.0064527 1
GO:0034154 BP toll-like receptor 7 signaling pathway 6 1 0.0069035 1
GO:0016209 MF antioxidant activity 83 2 0.0069530 1
GO:0021935 BP cerebellar granule cell precursor tangential migration 2 1 0.0070459 1
GO:0016206 MF catechol O-methyltransferase activity 2 1 0.0071794 1
GO:0102084 MF L-dopa O-methyltransferase activity 2 1 0.0071794 1
GO:0102938 MF orcinol O-methyltransferase activity 2 1 0.0071794 1
GO:0072301 BP regulation of metanephric glomerular mesangial cell proliferation 2 1 0.0072438 1
GO:0051377 MF mannose-ethanolamine phosphotransferase activity 3 1 0.0072565 1
GO:0045764 BP positive regulation of cellular amino acid metabolic process 3 1 0.0074539 1
GO:0042698 BP ovulation cycle 69 2 0.0075994 1
GO:0035814 BP negative regulation of renal sodium excretion 3 1 0.0078159 1
GO:0061032 BP visceral serous pericardium development 2 1 0.0078660 1
GO:0033238 BP regulation of cellular amine metabolic process 78 2 0.0080612 1
GO:0046501 BP protoporphyrinogen IX metabolic process 10 1 0.0081033 1
GO:0004416 MF hydroxyacylglutathione hydrolase activity 2 1 0.0083624 1
GO:0019243 BP methylglyoxal catabolic process to D-lactate via S-lactoyl-glutathione 2 1 0.0083624 1
GO:0051596 BP methylglyoxal catabolic process 2 1 0.0083624 1
GO:0061727 BP methylglyoxal catabolic process to lactate 2 1 0.0083624 1
GO:0072262 BP metanephric glomerular mesangial cell proliferation involved in metanephros development 3 1 0.0088988 1
GO:0051176 BP positive regulation of sulfur metabolic process 3 1 0.0090728 1
GO:0072166 BP posterior mesonephric tubule development 2 1 0.0095614 1
GO:0021934 BP hindbrain tangential cell migration 3 1 0.0097382 1
GO:0070181 MF small ribosomal subunit rRNA binding 10 1 0.0101955 1
GO:0035801 BP adrenal cortex development 2 1 0.0103000 1
GO:0035802 BP adrenal cortex formation 2 1 0.0103000 1
GO:0098869 BP cellular oxidant detoxification 96 2 0.0105889 1
GO:2001074 BP regulation of metanephric ureteric bud development 2 1 0.0107573 1
GO:2001076 BP positive regulation of metanephric ureteric bud development 2 1 0.0107573 1
GO:1990748 BP cellular detoxification 105 2 0.0114517 1
GO:1905643 BP positive regulation of DNA methylation 3 1 0.0119423 1
GO:0016013 CC syntrophin complex 3 1 0.0122287 1
GO:1903527 BP positive regulation of membrane tubulation 4 1 0.0122956 1
GO:0034164 BP negative regulation of toll-like receptor 9 signaling pathway 3 1 0.0125471 1
GO:0009438 BP methylglyoxal metabolic process 5 1 0.0125610 1
GO:0032687 BP negative regulation of interferon-alpha production 6 1 0.0126305 1
GO:0044729 MF hemi-methylated DNA-binding 3 1 0.0131488 1
GO:0042420 BP dopamine catabolic process 5 1 0.0131948 1
GO:0010385 MF double-stranded methylated DNA binding 4 1 0.0132070 1
GO:0044106 BP cellular amine metabolic process 119 2 0.0137636 1
GO:0042182 BP ketone catabolic process 9 1 0.0140733 1
GO:0071535 MF RING-like zinc finger domain binding 4 1 0.0142495 1
GO:0036353 BP histone H2A-K119 monoubiquitination 8 1 0.0144099 1
GO:0072223 BP metanephric glomerular mesangium development 5 1 0.0144316 1
GO:2000195 BP negative regulation of female gonad development 5 1 0.0144413 1
GO:0045914 BP negative regulation of catecholamine metabolic process 4 1 0.0147543 1
GO:0045963 BP negative regulation of dopamine metabolic process 4 1 0.0147543 1
GO:1903525 BP regulation of membrane tubulation 6 1 0.0153190 1
GO:0009308 BP amine metabolic process 128 2 0.0153320 1
GO:0072125 BP negative regulation of glomerular mesangial cell proliferation 4 1 0.0154115 1
GO:0090194 BP negative regulation of glomerulus development 4 1 0.0154115 1
GO:0019614 BP catechol-containing compound catabolic process 6 1 0.0155222 1
GO:0042424 BP catecholamine catabolic process 6 1 0.0155222 1
GO:0098754 BP detoxification 129 2 0.0158916 1
GO:0007356 BP thorax and anterior abdomen determination 5 1 0.0168477 1
GO:0007614 BP short-term memory 9 1 0.0176631 1
GO:0001547 BP antral ovarian follicle growth 8 1 0.0178660 1
GO:0008585 BP female gonad development 92 2 0.0180206 1
GO:0034163 BP regulation of toll-like receptor 9 signaling pathway 8 1 0.0185349 1
GO:0044703 BP multi-organism reproductive process 911 5 0.0185365 1
GO:1905940 BP negative regulation of gonad development 6 1 0.0186027 1
GO:0019336 BP phenol-containing compound catabolic process 9 1 0.0187532 1
GO:0072298 BP regulation of metanephric glomerulus development 5 1 0.0188366 1
GO:0046185 BP aldehyde catabolic process 11 1 0.0190056 1
GO:0035502 BP metanephric part of ureteric bud development 6 1 0.0190321 1
GO:0004791 MF thioredoxin-disulfide reductase activity 7 1 0.0191359 1
GO:0051537 MF 2 iron, 2 sulfur cluster binding 21 1 0.0194764 1
GO:0018958 BP phenol-containing compound metabolic process 94 2 0.0196449 1
GO:0046545 BP development of primary female sexual characteristics 96 2 0.0201548 1
GO:0033240 BP positive regulation of cellular amine metabolic process 7 1 0.0210294 1
GO:0016668 MF oxidoreductase activity, acting on a sulfur group of donors, NAD(P) as acceptor 11 1 0.0220457 1
GO:0072284 BP metanephric S-shaped body morphogenesis 6 1 0.0220657 1
GO:0048511 BP rhythmic process 286 3 0.0222464 1
GO:0007354 BP zygotic determination of anterior/posterior axis, embryo 6 1 0.0227852 1
GO:0035372 BP protein localization to microtubule 14 1 0.0228225 1
GO:0033239 BP negative regulation of cellular amine metabolic process 7 1 0.0229552 1

With cell type adjustment

Blood only

metal_blood_cell_DVP = read.table('/Users/annebozack/Documents/arsenic_meta/generic-metal/blood_cell_common_DVP_1204201.tbl', sep = "\t")

metal_blood_cell_DVP = metalProcess(metal_blood_cell_DVP)

write.csv(metal_blood_cell_DVP, '/Users/annebozack/Documents/arsenic_meta/generic-metal/DVP_blood_cell_common_120420.csv')


# Significant probes

# Nominal P-value
table(metal_blood_cell_DVP$P.value < 0.05)
#  FALSE   TRUE 
# 348773  28578 

# FDR
table(metal_blood_cell_DVP$P.FDR < 0.05)
#  FALSE   TRUE 
# 377328     23 

table(metal_blood_cell_DVP$P.FDR < 0.1)
#  FALSE   TRUE 
# 377266     85 

# Bonferroni
table(metal_blood_cell_DVP$P.Bonf < 0.05)
#  FALSE   TRUE 
#  377347      4 


# GO analysis, FDR < 0.1 probes

go_metal_blood_cell_DVP = gometh(sig.cpg = metal_blood_cell_DVP$Name[metal_blood_cell_DVP$P.FDR < 0.1], all.cpg = metal_blood_cell_DVP$Name, array.type = '450K', anno = annAll2)
go_metal_blood_cell_DVP = go_metal_blood_cell_DVP[order(go_metal_blood_cell_DVP$P.DE),]

table(go_metal_blood_cell_DVP$P.DE<0.05)
# FALSE  TRUE 
# 22282   301 

table(go_metal_blood_cell_DVP$FDR<0.05)
# FALSE 
# 22583 

write.csv(go_metal_blood_cell_DVP[go_metal_blood_cell_DVP$P.DE<0.05,], '/Users/annebozack/Documents/arsenic_meta/generic-metal/GO_DVP_blood_cell_common_120420.csv')


# KEGG analysis, FDR < 0.1 probes

kegg_metal_blood_cell_DVP = gometh(sig.cpg = metal_blood_cell_DVP$Name[metal_blood_cell_DVP$P.FDR < 0.1], all.cpg = metal_blood_cell_DVP$Name, array.type = '450K', collection = 'KEGG', sig.genes = T, anno = annAll2)
kegg_metal_blood_cell_DVP = kegg_metal_blood_cell_DVP[order(kegg_metal_blood_cell_DVP$P.DE),]

table(kegg_metal_blood_cell_DVP$P.DE<0.05)
# FALSE  TRUE 
# 335     5 

table(kegg_metal_blood_cell_DVP$FDR<0.05)
# FALSE 
# 340 

write.csv(kegg_metal_blood_cell_DVP[kegg_metal_blood_cell_DVP$P.DE<0.05,], '/Users/annebozack/Documents/arsenic_meta/generic-metal/KEGG_DVP_blood_cell_common_120420.csv')




# Plotting

gg_qqplot(metal_blood_cell_DVP$P.value)
quartz.save('qq_metal_blood_cell_DVP_120420.png', type = "png", dpi = 300)

manhattan_meta(metal_blood_cell_DVP, FDR=T)
quartz.save('manhattan_metal_blood_cell_DVP_120420.png', type = "png", dpi = 300)

volcano_meta(metal_blood_cell_DVP, FDR = TRUE)
quartz.save('volcano_metal_blood_cell_DVP_120420.png', type = "png", dpi = 300)
knitr::include_graphics("/Users/annebozack/Documents/arsenic_meta/generic-metal/qq_metal_blood_cell_DVP_120420.png")

knitr::include_graphics("/Users/annebozack/Documents/arsenic_meta/generic-metal/manhattan_metal_blood_cell_DVP_120420.png")

knitr::include_graphics("/Users/annebozack/Documents/arsenic_meta/generic-metal/volcano_metal_blood_cell_DVP_120420.png")

Top 100 probes

X Name Effect StdErr P.value Direction P.FDR P.Bonf chr pos UCSC_RefGene_Name UCSC_RefGene_Group
321132 cg23281729 0.9728 0.1462 0.00e+00 -++ 0.0000108 0.0000108 chr18 78005477 PARD6G TSS200
374163 cg27425262 0.8238 0.1473 0.00e+00 +++ 0.0042584 0.0085168 chr2 113953981 PSD4;LOC440839 Body;Body
167567 cg11361658 0.1740 0.0323 1.00e-07 +++ 0.0087332 0.0261995 chr5 128452311
50934 cg03205258 0.6862 0.1287 1.00e-07 +++ 0.0091725 0.0366898 chr22 19929274 TXNRD2;COMT;COMT 1stExon;1stExon;5’UTR
145256 cg09692492 -0.3502 0.0664 1.00e-07 0.0102489 0.0512443 chr22 23744717 ZDHHC8P Body
163279 cg11032634 0.7694 0.1503 3.00e-07 +++ 0.0192135 0.1152807 chr22 19929254 TXNRD2;COMT 1stExon;TSS200
237588 cg16511076 0.1302 0.0257 4.00e-07 +++ 0.0219295 0.1535064 chr4 48887480 OCIAD2;OCIAD2 3’UTR;3’UTR
309909 cg22387890 0.5501 0.1098 5.00e-07 +++ 0.0228562 0.2051280 chr7 6145595 USP42 5’UTR
314099 cg22749736 0.1312 0.0262 6.00e-07 +++ 0.0228562 0.2087506 chr11 1306759 TOLLIP Body
64158 cg04080724 0.1387 0.0278 6.00e-07 +++ 0.0228562 0.2285615 chr4 140202327 C4orf49 TSS1500
80568 cg05169951 0.2307 0.0465 7.00e-07 +++ 0.0239892 0.2638816 chr16 3017955 KREMEN2;PAQR4;KREMEN2 Body;TSS1500;Body
11224 cg00668103 0.1440 0.0292 8.00e-07 +++ 0.0254209 0.3050505 chr7 100084730 C7orf51 Body
124685 cg08207566 0.1245 0.0255 1.00e-06 +++ 0.0303042 0.3939544 chr4 174086461
18303 cg01101647 0.1337 0.0275 1.10e-06 +++ 0.0303228 0.4245199 chr4 66535732 EPHA5;EPHA5 TSS200;TSS200
116190 cg07611790 0.1053 0.0217 1.30e-06 +++ 0.0309847 0.4724435 chr19 49240823 RASIP1 Body
171628 cg11691429 0.2056 0.0426 1.40e-06 +++ 0.0309847 0.5248952 chr2 947634 SNTG2 Body
295936 cg21185289 0.3802 0.0789 1.50e-06 +++ 0.0309847 0.5471590 chr2 74743437 TLX2 3’UTR
125889 cg08285768 0.1113 0.0231 1.50e-06 +++ 0.0309847 0.5577248 chr15 86038622 AKAP13;AKAP13 Body;Body
202666 cg13972353 0.1460 0.0304 1.60e-06 +++ 0.0311811 0.5924411 chr9 139354348 SEC16A Body
102811 cg06740986 0.1067 0.0225 2.10e-06 +++ 0.0392634 0.7852674 chr1 184838417 FAM129A Body
303849 cg21857098 0.1220 0.0259 2.50e-06 +++ 0.0428636 0.9286608 chr15 25638137 UBE3A;UBE3A;UBE3A Body;Body;Body
55105 cg03479942 0.1266 0.0269 2.50e-06 +++ 0.0428636 0.9430001 chr16 69341763 SNTB2 3’UTR
121453 cg07984508 0.1050 0.0224 2.70e-06 +++ 0.0447243 1.0000000 chr15 77426719 SGK269 Body
168599 cg11440940 0.1144 0.0246 3.30e-06 +++ 0.0509569 1.0000000 chr19 8510764 HNRNPM;HNRNPM Body;Body
150964 cg10117884 0.1325 0.0285 3.40e-06 +++ 0.0509569 1.0000000 chr1 166955898
308533 cg22267402 0.1390 0.0300 3.50e-06 +++ 0.0509569 1.0000000 chr22 44463707 PARVB;PARVB Body;Body
100415 cg06581201 0.2001 0.0434 4.00e-06 +++ 0.0529265 1.0000000 chr6 168534038
248409 cg17332762 0.1085 0.0236 4.20e-06 +++ 0.0529265 1.0000000 chr3 106967639 LOC344595;LOC344595 Body;Body
93087 cg06039392 0.1497 0.0325 4.20e-06 +++ 0.0529265 1.0000000 chr4 187476953 MTNR1A TSS1500
58507 cg03700279 0.1118 0.0243 4.20e-06 +++ 0.0529265 1.0000000 chr2 44576358 PREPL;PREPL;PREPL;PREPL;PREPL;PREPL;PREPL Body;Body;5’UTR;5’UTR;Body;Body;Body
32578 cg02026246 0.1671 0.0364 4.30e-06 +++ 0.0529265 1.0000000 chr11 22687589 GAS2 TSS1500
373469 cg27371984 0.2504 0.0547 4.80e-06 +++ 0.0561545 1.0000000 chr17 78009155 CCDC40;TBC1D16 TSS1500;5’UTR
156274 cg10502904 0.1806 0.0396 5.10e-06 +++ 0.0582035 1.0000000 chr10 131565289 MGMT 3’UTR
208658 cg14332223 0.1916 0.0421 5.30e-06 –+ 0.0592108 1.0000000 chr19 56136067 ZNF784 TSS200
129911 cg08575722 -0.1446 0.0318 5.50e-06 0.0595244 1.0000000 chr11 32421845 WT1;WT1;WT1;WT1 Body;Body;Body;Body
120767 cg07935287 -0.1377 0.0304 5.80e-06 0.0605019 1.0000000 chr18 54318347 WDR7;WDR7 TSS1500;TSS1500
25526 cg01570086 -0.1467 0.0325 6.20e-06 0.0633032 1.0000000 chr15 74833080 ARID3B TSS1500
110491 cg07219314 -0.1929 0.0428 6.60e-06 0.0645540 1.0000000 chr22 23744725 ZDHHC8P Body
199880 cg13797228 0.1106 0.0246 7.00e-06 -++ 0.0645540 1.0000000 chr3 126076243 KLF15 TSS200
214646 cg14718822 -0.1749 0.0389 7.10e-06 -+- 0.0645540 1.0000000 chr6 84234250 PRSS35;PRSS35 Body;Body
156000 cg10485752 0.1511 0.0337 7.20e-06 +++ 0.0645540 1.0000000 chr1 26021655 MAN1C1 Body
109701 cg07168204 0.1274 0.0284 7.20e-06 +++ 0.0645540 1.0000000 chr5 149864599
10618 cg00629117 0.7703 0.1719 7.40e-06 +++ 0.0650448 1.0000000 chr16 1844932 IGFALS;IGFALS;IGFALS TSS200;TSS1500;TSS1500
11047 cg00657529 0.0977 0.0219 8.00e-06 +++ 0.0684034 1.0000000 chr6 31698687 CLIC1;DDAH2 Body;TSS1500
227727 cg15754901 0.1165 0.0261 8.30e-06 +-+ 0.0692900 1.0000000 chr17 5402972 LOC728392 3’UTR
320947 cg23268677 0.3213 0.0723 8.70e-06 +++ 0.0717705 1.0000000 chr22 19929097 TXNRD2;COMT Body;TSS200
293675 cg21004290 0.1299 0.0293 9.00e-06 +++ 0.0719697 1.0000000 chr8 131250320 ASAP1 Body
324700 cg23574838 0.0719 0.0163 1.01e-05 +++ 0.0778535 1.0000000 chr20 3186475 DDRGK1 TSS1500
132616 cg08770961 0.3268 0.0741 1.03e-05 +++ 0.0778535 1.0000000 chr16 66956122 RRAD;RRAD Body;Body
316511 cg22938135 0.0961 0.0218 1.06e-05 +++ 0.0778535 1.0000000 chr5 175841493 CLTB;CLTB Body;Body
107264 cg07018132 0.0975 0.0222 1.10e-05 +++ 0.0778535 1.0000000 chr16 718091 RHOT2 TSS200
281026 cg19929852 0.1226 0.0279 1.10e-05 +++ 0.0778535 1.0000000 chr4 15068643 CPEB2;CPEB2 3’UTR;3’UTR
351734 cg25721832 0.0929 0.0212 1.12e-05 +++ 0.0778535 1.0000000 chr3 81913557
268961 cg18971529 0.3043 0.0693 1.15e-05 ++- 0.0778535 1.0000000 chr21 30391563 RWDD2B 1stExon
198387 cg13698261 0.1019 0.0232 1.15e-05 +++ 0.0778535 1.0000000 chr9 97841956 C9orf3 Body
109543 cg07159858 -0.1358 0.0310 1.16e-05 +– 0.0778535 1.0000000 chr14 75744601 FOS TSS1500
62770 cg03988518 0.1819 0.0415 1.18e-05 ++- 0.0778535 1.0000000 chr6 170763536
149284 cg09996597 0.4310 0.0985 1.22e-05 +++ 0.0781745 1.0000000 chr16 1844927 IGFALS;IGFALS;IGFALS TSS200;TSS1500;TSS1500
51985 cg03277137 0.0799 0.0183 1.22e-05 +++ 0.0781745 1.0000000 chr13 113513653 ATP11A;ATP11A Body;Body
120984 cg07952047 0.1885 0.0431 1.24e-05 +++ 0.0781745 1.0000000 chr19 54024110 ZNF331 TSS200
35145 cg02192228 0.1987 0.0455 1.29e-05 +++ 0.0791857 1.0000000 chr3 8809536 OXTR Body
178342 cg12175949 0.3943 0.0906 1.35e-05 +++ 0.0791857 1.0000000 chr22 19929286 TXNRD2;COMT;COMT 1stExon;1stExon;5’UTR
259615 cg18228116 0.3740 0.0860 1.36e-05 -++ 0.0791857 1.0000000 chr10 133995345 JAKMIP3 3’UTR
114654 cg07510163 0.1646 0.0378 1.36e-05 +++ 0.0791857 1.0000000 chr2 44547313 PREPL;PREPL;PREPL;PREPL;PREPL;PREPL;SLC3A1;PREPL 3’UTR;3’UTR;3’UTR;3’UTR;3’UTR;3’UTR;Body;3’UTR
282819 cg20074307 0.0870 0.0200 1.36e-05 +++ 0.0791857 1.0000000 chr14 55092491 SAMD4A;SAMD4A Body;Body
169144 cg11494866 0.1107 0.0255 1.39e-05 +++ 0.0794152 1.0000000 chr8 42695070 THAP1;THAP1 Body;Body
271236 cg19170881 -0.1888 0.0435 1.42e-05 0.0802012 1.0000000 chr7 101129980 EMID2 Body
351392 cg25691442 0.1096 0.0253 1.46e-05 +++ 0.0812969 1.0000000 chr15 63345512 TPM1;TPM1;TPM1;TPM1;TPM1;TPM1;TPM1 Body;Body;Body;Body;Body;Body;Body
138885 cg09235788 0.1447 0.0335 1.57e-05 +++ 0.0859704 1.0000000 chr1 111220207
370643 cg27155653 -0.1124 0.0261 1.61e-05 0.0867907 1.0000000 chr1 183604774 ARPC5;RGL1 1stExon;TSS1500
351214 cg25674826 0.2883 0.0670 1.71e-05 +++ 0.0906705 1.0000000 chr21 35446543 MRPS6;SLC5A3 Body;5’UTR
148318 cg09920145 -0.1037 0.0241 1.76e-05 0.0923986 1.0000000 chr3 69100714 TMF1 Body
232066 cg16101346 0.1755 0.0409 1.79e-05 -++ 0.0924251 1.0000000 chr1 186650479 PTGS2 TSS1500
343712 cg25052374 0.0833 0.0194 1.83e-05 +++ 0.0935728 1.0000000 chr17 76991253 CANT1;CANT1;CANT1 Body;Body;Body
207024 cg14231959 0.1401 0.0327 1.90e-05 +++ 0.0940895 1.0000000 chr8 1897035 ARHGEF10 Body
222184 cg15317815 0.2440 0.0570 1.90e-05 +++ 0.0940895 1.0000000 chr3 8809306 OXTR Body
349119 cg25499746 0.0878 0.0205 1.94e-05 +++ 0.0949748 1.0000000 chr6 16346054 ATXN1;ATXN1 5’UTR;5’UTR
114218 cg07479711 0.1174 0.0275 1.98e-05 +++ 0.0953886 1.0000000 chr5 1524940 LPCAT1 TSS1500
26498 cg01632803 0.1085 0.0254 2.00e-05 +++ 0.0953886 1.0000000 chr19 48891159 KDELR1 Body
127440 cg08400962 0.1223 0.0287 2.04e-05 +++ 0.0955490 1.0000000 chr19 34112316 CHST8;CHST8 TSS1500;TSS1500
64658 cg04111999 0.1037 0.0244 2.05e-05 +++ 0.0955490 1.0000000 chr10 22615540 BMI1 Body
265593 cg18703721 0.1274 0.0299 2.10e-05 +++ 0.0966387 1.0000000 chr10 75282672 USP54 Body
41686 cg02608453 0.1053 0.0248 2.20e-05 +++ 0.0986884 1.0000000 chr9 125241447 OR1J1 TSS1500
161566 cg10898607 -0.1150 0.0271 2.20e-05 0.0986884 1.0000000 chr3 101405733 RPL24 TSS200
377087 cg27647852 0.0989 0.0233 2.22e-05 +++ 0.0986884 1.0000000 chr20 44036899 DBNDD2;DBNDD2;DBNDD2;SYS1-DBNDD2;DBNDD2;DBNDD2;DBNDD2 5’UTR;5’UTR;TSS200;Body;5’UTR;5’UTR;TSS200
181408 cg12433479 0.1713 0.0405 2.38e-05 +++ 0.1031703 1.0000000 chr3 38683662 SCN5A;SCN5A;SCN5A;SCN5A;SCN5A;SCN5A 5’UTR;5’UTR;5’UTR;5’UTR;5’UTR;5’UTR
111585 cg07297467 0.1250 0.0296 2.42e-05 +++ 0.1031703 1.0000000 chr2 101635691 RPL31;TBC1D8 3’UTR;Body
317171 cg22988651 0.1333 0.0316 2.43e-05 +++ 0.1031703 1.0000000 chr3 15792635 ANKRD28 Body
26185 cg01614020 0.2810 0.0666 2.44e-05 +++ 0.1031703 1.0000000 chr8 24814137 NEFL TSS200
190817 cg13208054 0.0820 0.0194 2.47e-05 +++ 0.1031703 1.0000000 chr17 25936354 KSR1 Body
153219 cg10273420 -0.0916 0.0217 2.49e-05 -+- 0.1031703 1.0000000 chr10 43953760 ZNF487 Body
308465 cg22261158 0.1292 0.0307 2.53e-05 +++ 0.1037305 1.0000000 chr12 98941654 TMPO;TMPO 3’UTR;3’UTR
201631 cg13909585 0.2349 0.0559 2.61e-05 +++ 0.1041717 1.0000000 chr7 82792379 PCLO;PCLO TSS200;TSS200
240114 cg16681246 0.0937 0.0223 2.62e-05 +++ 0.1041717 1.0000000 chr2 65541310 SPRED2;SPRED2 Body;Body
131033 cg08654960 -0.1464 0.0348 2.63e-05 0.1041717 1.0000000 chr16 85319859
31762 cg01972350 -0.1407 0.0335 2.68e-05 0.1041717 1.0000000 chr17 79155695 LOC388428 Body
150911 cg10114235 0.1228 0.0293 2.69e-05 +++ 0.1041717 1.0000000 chr6 169449059
47856 cg02996181 0.0722 0.0172 2.71e-05 ++- 0.1041717 1.0000000 chr11 417643 SIGIRR;SIGIRR TSS1500;TSS1500
199205 cg13751796 0.0845 0.0202 2.73e-05 +++ 0.1041717 1.0000000 chr9 132633833 USP20;USP20;USP20 Body;Body;Body
229928 cg15931233 0.1027 0.0245 2.77e-05 +++ 0.1046017 1.0000000 chr5 53455496 ARL15 Body

Top 100 GO terms

X ONTOLOGY TERM N DE P.DE FDR
GO:0048545 BP response to steroid hormone 329 8 0.0002538 1
GO:2000171 BP negative regulation of dendrite development 25 3 0.0006726 1
GO:0003044 BP regulation of systemic arterial blood pressure mediated by a chemical signal 45 3 0.0009954 1
GO:0070972 BP protein localization to endoplasmic reticulum 134 4 0.0011312 1
GO:0009725 BP response to hormone 863 12 0.0013203 1
GO:0032570 BP response to progesterone 45 3 0.0015462 1
GO:0031307 CC integral component of mitochondrial outer membrane 19 2 0.0030355 1
GO:0099631 CC postsynaptic endocytic zone cytoplasmic component 2 1 0.0031890 1
GO:0031306 CC intrinsic component of mitochondrial outer membrane 20 2 0.0034739 1
GO:0071383 BP cellular response to steroid hormone stimulus 194 5 0.0035536 1
GO:0030728 BP ovulation 20 2 0.0035557 1
GO:0050774 BP negative regulation of dendrite morphogenesis 14 2 0.0039691 1
GO:0006979 BP response to oxidative stress 434 7 0.0040529 1
GO:0061000 BP negative regulation of dendritic spine development 11 2 0.0041920 1
GO:0004990 MF oxytocin receptor activity 1 1 0.0046387 1
GO:0006305 BP DNA alkylation 71 3 0.0047397 1
GO:0006306 BP DNA methylation 71 3 0.0047397 1
GO:0016010 CC dystrophin-associated glycoprotein complex 18 2 0.0047560 1
GO:0090665 CC glycoprotein complex 18 2 0.0047560 1
GO:0061318 BP renal filtration cell differentiation 18 2 0.0051905 1
GO:0072112 BP glomerular visceral epithelial cell differentiation 18 2 0.0051905 1
GO:0050886 BP endocrine process 78 3 0.0054921 1
GO:0010335 BP response to non-ionic osmotic stress 1 1 0.0056612 1
GO:0071471 BP cellular response to non-ionic osmotic stress 1 1 0.0056612 1
GO:0007613 BP memory 116 4 0.0056747 1
GO:1903524 BP positive regulation of blood circulation 72 3 0.0056822 1
GO:0072311 BP glomerular epithelial cell differentiation 19 2 0.0057171 1
GO:0044703 BP multi-organism reproductive process 943 10 0.0062853 1
GO:0072010 BP glomerular epithelium development 22 2 0.0066983 1
GO:0043401 BP steroid hormone mediated signaling pathway 131 4 0.0067175 1
GO:0004666 MF prostaglandin-endoperoxide synthase activity 2 1 0.0070536 1
GO:0090362 BP positive regulation of platelet-derived growth factor production 2 1 0.0073248 1
GO:0034643 BP establishment of mitochondrion localization, microtubule-mediated 22 2 0.0074343 1
GO:0047497 BP mitochondrion transport along microtubule 22 2 0.0074343 1
GO:0030371 MF translation repressor activity 24 2 0.0079009 1
GO:0003073 BP regulation of systemic arterial blood pressure 87 3 0.0079262 1
GO:0051654 BP establishment of mitochondrion localization 25 2 0.0086020 1
GO:0001990 BP regulation of systemic arterial blood pressure by hormone 35 2 0.0087258 1
GO:0007565 BP female pregnancy 175 4 0.0088200 1
GO:0008217 BP regulation of blood pressure 175 4 0.0088372 1
GO:0044728 BP DNA methylation or demethylation 94 3 0.0091241 1
GO:2000815 BP regulation of mRNA stability involved in response to oxidative stress 2 1 0.0091562 1
GO:0030660 CC Golgi-associated vesicle membrane 103 3 0.0091582 1
GO:0035037 BP sperm entry 1 1 0.0093095 1
GO:0061795 BP Golgi lumen acidification 1 1 0.0093095 1
GO:1905526 BP regulation of Golgi lumen acidification 1 1 0.0093095 1
GO:1905528 BP positive regulation of Golgi lumen acidification 1 1 0.0093095 1
GO:0030431 BP sleep 34 2 0.0098816 1
GO:0045987 BP positive regulation of smooth muscle contraction 31 2 0.0099122 1
GO:0031337 BP positive regulation of sulfur amino acid metabolic process 1 1 0.0099457 1
GO:0050668 BP positive regulation of homocysteine metabolic process 1 1 0.0099457 1
GO:0045777 BP positive regulation of blood pressure 37 2 0.0099634 1
GO:0051704 BP multi-organism process 1013 10 0.0100226 1
GO:0003065 BP positive regulation of heart rate by epinephrine 1 1 0.0103331 1
GO:0001992 BP regulation of systemic arterial blood pressure by vasopressin 4 1 0.0107040 1
GO:1905550 BP regulation of protein localization to endoplasmic reticulum 2 1 0.0108268 1
GO:1905552 BP positive regulation of protein localization to endoplasmic reticulum 2 1 0.0108268 1
GO:0005046 MF KDEL sequence binding 3 1 0.0108284 1
GO:0019098 BP reproductive behavior 30 2 0.0109375 1
GO:1905636 BP positive regulation of RNA polymerase II regulatory region sequence-specific DNA binding 3 1 0.0109386 1
GO:0035936 BP testosterone secretion 2 1 0.0111017 1
GO:2000843 BP regulation of testosterone secretion 2 1 0.0111017 1
GO:2000845 BP positive regulation of testosterone secretion 2 1 0.0111017 1
GO:0072299 BP negative regulation of metanephric glomerulus development 1 1 0.0111036 1
GO:0072302 BP negative regulation of metanephric glomerular mesangial cell proliferation 1 1 0.0111036 1
GO:0071284 BP cellular response to lead ion 3 1 0.0111855 1
GO:0035023 BP regulation of Rho protein signal transduction 79 3 0.0112261 1
GO:1903895 BP negative regulation of IRE1-mediated unfolded protein response 5 1 0.0114765 1
GO:0004382 MF guanosine-diphosphatase activity 2 1 0.0115044 1
GO:1902626 BP assembly of large subunit precursor of preribosome 3 1 0.0115739 1
GO:0047191 MF 1-alkylglycerophosphocholine O-acyltransferase activity 1 1 0.0117615 1
GO:2001246 BP negative regulation of phosphatidylcholine biosynthetic process 1 1 0.0117615 1
GO:0003908 MF methylated-DNA-[protein]-cysteine S-methyltransferase activity 1 1 0.0117914 1
GO:0043001 BP Golgi to plasma membrane protein transport 39 2 0.0120581 1
GO:0050666 BP regulation of homocysteine metabolic process 2 1 0.0125404 1
GO:0007612 BP learning 140 4 0.0126947 1
GO:0014070 BP response to organic cyclic compound 885 10 0.0129020 1
GO:0032870 BP cellular response to hormone stimulus 602 8 0.0133645 1
GO:0045907 BP positive regulation of vasoconstriction 33 2 0.0134807 1
GO:0006304 BP DNA modification 116 3 0.0138524 1
GO:1990564 BP protein polyufmylation 5 1 0.0138602 1
GO:1990592 BP protein K69-linked ufmylation 5 1 0.0138602 1
GO:0090360 BP platelet-derived growth factor production 3 1 0.0139227 1
GO:0090361 BP regulation of platelet-derived growth factor production 3 1 0.0139227 1
GO:0008585 BP female gonad development 96 3 0.0140875 1
GO:0047159 MF 1-alkenylglycerophosphocholine O-acyltransferase activity 2 1 0.0144966 1
GO:0050200 MF plasmalogen synthase activity 2 1 0.0144966 1
GO:0044706 BP multi-multicellular organism process 204 4 0.0146238 1
GO:0001544 BP initiation of primordial ovarian follicle growth 2 1 0.0151198 1
GO:0005150 MF interleukin-1, type I receptor binding 2 1 0.0152167 1
GO:0072301 BP regulation of metanephric glomerular mesangial cell proliferation 2 1 0.0155594 1
GO:1900169 BP regulation of glucocorticoid mediated signaling pathway 2 1 0.0155805 1
GO:0047192 MF 1-alkylglycerophosphocholine O-acetyltransferase activity 3 1 0.0156545 1
GO:0071963 BP establishment or maintenance of cell polarity regulating cell shape 2 1 0.0158844 1
GO:0045764 BP positive regulation of cellular amino acid metabolic process 3 1 0.0162795 1
GO:0016206 MF catechol O-methyltransferase activity 2 1 0.0163029 1
GO:0102084 MF L-dopa O-methyltransferase activity 2 1 0.0163029 1
GO:0102938 MF orcinol O-methyltransferase activity 2 1 0.0163029 1
GO:0046545 BP development of primary female sexual characteristics 100 3 0.0163060 1
GO:0034059 BP response to anoxia 3 1 0.0164205 1

Including buccal

metal_all_cell_DVP = read.table('/Users/annebozack/Documents/arsenic_meta/generic-metal/all_cell_common_DVP_1204201.tbl', sep = "\t")

metal_all_cell_DVP = metalProcess(metal_all_cell_DVP)

write.csv(metal_all_cell_DVP, '/Users/annebozack/Documents/arsenic_meta/generic-metal/DVP_all_cell_common_120420.csv')


# Significant probes

# Nominal P-value
table(metal_all_cell_DVP$P.value < 0.05)
#  FALSE   TRUE 
# 348952  28399 

# FDR
table(metal_all_cell_DVP$P.FDR < 0.05)
# FALSE   TRUE 
# 377332     19 

table(metal_all_cell_DVP$P.FDR < 0.1)
 # FALSE   TRUE 
# 377245    106 

# Bonferroni
table(metal_all_cell_DVP$P.Bonf < 0.05)
# FALSE     TRUE
# 377346      5 


# GO analysis, FDR < 0.1 probes

go_metal_all_cell_DVP = gometh(sig.cpg = metal_all_cell_DVP$Name[metal_all_cell_DVP$P.FDR < 0.1], all.cpg = metal_all_cell_DVP$Name, array.type = '450K', anno = annAll2)
go_metal_all_cell_DVP = go_metal_all_cell_DVP[order(go_metal_all_cell_DVP$P.DE),]

table(go_metal_all_cell_DVP$P.DE<0.05)
# FALSE  TRUE 
# 22314   269  

table(go_metal_all_cell_DVP$FDR<0.05)
# FALSE 
# 22583 

write.csv(go_metal_all_cell_DVP[go_metal_all_cell_DVP$P.DE<0.05,], '/Users/annebozack/Documents/arsenic_meta/generic-metal/GO_DVP_all_cell_common_120420.csv')


# KEGG analysis, FDR < 0.1 probes

kegg_metal_all_cell_DVP = gometh(sig.cpg = metal_all_cell_DVP$Name[metal_all_cell_DVP$P.FDR < 0.1], all.cpg = metal_all_cell_DVP$Name, array.type = '450K', collection = 'KEGG', sig.genes = T, anno = annAll2)
kegg_metal_all_cell_DVP = kegg_metal_all_cell_DVP[order(kegg_metal_all_cell_DVP$P.DE),]

table(kegg_metal_all_cell_DVP$P.DE<0.05)
# FALSE  TRUE 
#  336     4

table(kegg_metal_all_cell_DVP$FDR<0.05)
# FALSE 
# 340 

write.csv(kegg_metal_all_cell_DVP[kegg_metal_all_cell_DVP$P.DE < 0.05,], '/Users/annebozack/Documents/arsenic_meta/generic-metal/KEGG_DVP_all_cell_common_120420.csv')




# Plotting

gg_qqplot(metal_all_cell_DVP$P.value)
quartz.save('qq_metal_all_cell_DVP_120420.png', type = "png", dpi = 300)

manhattan_meta(metal_all_cell_DVP, FDR=T)
quartz.save('manhattan_metal_all_cell_DVP_120420.png', type = "png", dpi = 300)

volcano_meta(metal_all_cell_DVP, FDR = TRUE)
quartz.save('volcano_metal_all_cell_DVP_120420.png', type = "png", dpi = 300)
knitr::include_graphics("/Users/annebozack/Documents/arsenic_meta/generic-metal/qq_metal_all_cell_DVP_120420.png")

knitr::include_graphics("/Users/annebozack/Documents/arsenic_meta/generic-metal/manhattan_metal_all_cell_DVP_120420.png")

knitr::include_graphics("/Users/annebozack/Documents/arsenic_meta/generic-metal/volcano_metal_all_cell_DVP_120420.png")

Top 100 probes

X Name Effect StdErr P.value Direction P.FDR P.Bonf chr pos UCSC_RefGene_Name UCSC_RefGene_Group
321132 cg23281729 0.9945 0.1300 0.00e+00 -+++ 0.0000000 0.0000000 chr18 78005477 PARD6G TSS200
374163 cg27425262 0.8952 0.1237 0.00e+00 ++++ 0.0000001 0.0000002 chr2 113953981 PSD4;LOC440839 Body;Body
50934 cg03205258 0.6446 0.1117 0.00e+00 ++++ 0.0010001 0.0030003 chr22 19929274 TXNRD2;COMT;COMT 1stExon;1stExon;5’UTR
163279 cg11032634 0.6967 0.1285 1.00e-07 ++++ 0.0056225 0.0224901 chr22 19929254 TXNRD2;COMT 1stExon;TSS200
64158 cg04080724 0.1394 0.0263 1.00e-07 ++++ 0.0085810 0.0429048 chr4 140202327 C4orf49 TSS1500
360213 cg26384602 -0.1222 0.0234 2.00e-07 —- 0.0102424 0.0705646 chr19 41798386 HNRNPUL1;HNRNPUL1 Body;Body
167567 cg11361658 0.1562 0.0300 2.00e-07 ++++ 0.0102424 0.0716967 chr5 128452311
145256 cg09692492 -0.2979 0.0576 2.00e-07 —- 0.0109290 0.0874322 chr22 23744717 ZDHHC8P Body
314099 cg22749736 0.1176 0.0232 4.00e-07 ++++ 0.0175929 0.1583365 chr11 1306759 TOLLIP Body
304645 cg21921619 -0.1465 0.0292 5.00e-07 -+– 0.0206675 0.2066751 chr10 116852791 ATRNL1 TSS1500
120767 cg07935287 -0.1330 0.0269 8.00e-07 —- 0.0257416 0.2984469 chr18 54318347 WDR7;WDR7 TSS1500;TSS1500
80568 cg05169951 0.2169 0.0440 8.00e-07 ++++ 0.0257416 0.3088995 chr16 3017955 KREMEN2;PAQR4;KREMEN2 Body;TSS1500;Body
295936 cg21185289 0.3705 0.0758 1.00e-06 ++++ 0.0293463 0.3815019 chr2 74743437 TLX2 3’UTR
309909 cg22387890 0.4772 0.0980 1.10e-06 ++++ 0.0302689 0.4237652 chr7 6145595 USP42 5’UTR
190387 cg13171197 0.1174 0.0244 1.50e-06 +-++ 0.0366266 0.5524419 chr7 90916020
339841 cg24754507 -0.1026 0.0214 1.60e-06 —- 0.0366266 0.5860261 chr6 28481862 GPX6 Body
5963 cg00355447 0.1410 0.0295 1.80e-06 ++++ 0.0392864 0.6792318 chr6 30292220 HCG18;HCG18 Body;Body
237588 cg16511076 0.1215 0.0255 1.90e-06 +++- 0.0392864 0.7071558 chr4 48887480 OCIAD2;OCIAD2 3’UTR;3’UTR
76120 cg04873963 -0.1029 0.0218 2.50e-06 —- 0.0487577 0.9263967 chr16 2518322
124685 cg08207566 0.1154 0.0246 2.80e-06 +++- 0.0533763 1.0000000 chr4 174086461
102811 cg06740986 0.0989 0.0213 3.30e-06 ++++ 0.0588488 1.0000000 chr1 184838417 FAM129A Body
167176 cg11332363 0.2113 0.0456 3.50e-06 ++++ 0.0598616 1.0000000 chr19 54023999 ZNF331 TSS200
302848 cg21774561 0.1147 0.0248 3.70e-06 ++++ 0.0604862 1.0000000 chr17 80209247 CSNK1D;CSNK1D Body;Body
219690 cg15104380 -0.0861 0.0186 3.80e-06 +— 0.0604862 1.0000000 chr10 99285205 UBTD1 Body
303849 cg21857098 0.1019 0.0222 4.60e-06 ++++ 0.0647340 1.0000000 chr15 25638137 UBE3A;UBE3A;UBE3A Body;Body;Body
293675 cg21004290 0.1266 0.0277 4.80e-06 ++++ 0.0647340 1.0000000 chr8 131250320 ASAP1 Body
193559 cg13411311 -0.1008 0.0220 4.80e-06 —- 0.0647340 1.0000000 chr2 241095989
161566 cg10898607 -0.1144 0.0250 4.80e-06 —- 0.0647340 1.0000000 chr3 101405733 RPL24 TSS200
129911 cg08575722 -0.1427 0.0313 5.10e-06 —- 0.0647340 1.0000000 chr11 32421845 WT1;WT1;WT1;WT1 Body;Body;Body;Body
189046 cg13054212 0.0959 0.0211 5.30e-06 ++++ 0.0647340 1.0000000 chr4 186356202 C4orf47 Body
214646 cg14718822 -0.1498 0.0329 5.30e-06 -+– 0.0647340 1.0000000 chr6 84234250 PRSS35;PRSS35 Body;Body
28677 cg01783101 0.2343 0.0517 5.80e-06 ++++ 0.0653810 1.0000000 chr7 118498931
334867 cg24376022 0.1055 0.0233 6.10e-06 ++++ 0.0653810 1.0000000 chr2 3215598 TSSC1 Body
11047 cg00657529 0.0940 0.0208 6.30e-06 ++++ 0.0653810 1.0000000 chr6 31698687 CLIC1;DDAH2 Body;TSS1500
191734 cg13281248 0.1068 0.0237 6.50e-06 ++++ 0.0653810 1.0000000 chr4 1244360 C4orf42;CTBP1;CTBP1;C4orf42 5’UTR;TSS1500;TSS1500;1stExon
179110 cg12235073 0.1203 0.0267 6.50e-06 ++-+ 0.0653810 1.0000000 chr10 6270423 PFKFB3;PFKFB3 Body;Body
243979 cg16991858 0.0921 0.0204 6.60e-06 ++++ 0.0653810 1.0000000 chr1 244612113 ADSS Body
337569 cg24587312 -0.0682 0.0151 6.60e-06 ++– 0.0653810 1.0000000 chr15 39766341
282709 cg20066496 -0.1849 0.0411 6.80e-06 +— 0.0654478 1.0000000 chr15 43213993 TTBK2 TSS1500
271236 cg19170881 -0.1914 0.0427 7.30e-06 —- 0.0654478 1.0000000 chr7 101129980 EMID2 Body
150964 cg10117884 0.1224 0.0273 7.40e-06 ++++ 0.0654478 1.0000000 chr1 166955898
162593 cg10980774 0.1646 0.0368 7.50e-06 ++++ 0.0654478 1.0000000 chr11 112832547 NCAM1;NCAM1;NCAM1 Body;Body;Body
119872 cg07875335 0.2405 0.0537 7.60e-06 ++++ 0.0654478 1.0000000 chr2 48844728 GTF2A1L;GTF2A1L;STON1-GTF2A1L TSS1500;TSS1500;Body
126025 cg08293531 -0.0993 0.0222 7.80e-06 —- 0.0654478 1.0000000 chr15 101601180 LRRK1 Body
140791 cg09366379 -0.2971 0.0666 8.20e-06 —- 0.0654478 1.0000000 chr16 87905824
116190 cg07611790 0.0956 0.0215 8.40e-06 +++- 0.0654478 1.0000000 chr19 49240823 RASIP1 Body
292637 cg20923605 0.3039 0.0682 8.40e-06 ++++ 0.0654478 1.0000000 chr13 112978683
188976 cg13049359 0.1933 0.0434 8.50e-06 +-++ 0.0654478 1.0000000 chr4 188891490
159378 cg10729167 0.1545 0.0347 8.60e-06 ++++ 0.0654478 1.0000000 chr10 111220101
23625 cg01445793 0.1912 0.0430 8.70e-06 ++++ 0.0654478 1.0000000 chr17 3771578 CAMKK1;CAMKK1;CAMKK1 Body;Body;Body
265593 cg18703721 0.1163 0.0262 9.40e-06 ++++ 0.0660776 1.0000000 chr10 75282672 USP54 Body
202666 cg13972353 0.1266 0.0286 9.50e-06 +++- 0.0660776 1.0000000 chr9 139354348 SEC16A Body
178342 cg12175949 0.3017 0.0682 9.60e-06 ++++ 0.0660776 1.0000000 chr22 19929286 TXNRD2;COMT;COMT 1stExon;1stExon;5’UTR
148318 cg09920145 -0.0958 0.0216 9.60e-06 —- 0.0660776 1.0000000 chr3 69100714 TMF1 Body
125889 cg08285768 0.1000 0.0226 9.60e-06 +++- 0.0660776 1.0000000 chr15 86038622 AKAP13;AKAP13 Body;Body
144882 cg09664373 0.1149 0.0260 1.01e-05 ++++ 0.0661963 1.0000000 chr16 968219 LMF1 Body
232066 cg16101346 0.1496 0.0339 1.03e-05 -+++ 0.0661963 1.0000000 chr1 186650479 PTGS2 TSS1500
300598 cg21575923 -0.1390 0.0315 1.03e-05 —- 0.0661963 1.0000000 chr6 41139345
110491 cg07219314 -0.1723 0.0391 1.03e-05 —- 0.0661963 1.0000000 chr22 23744725 ZDHHC8P Body
18378 cg01105932 0.1049 0.0239 1.17e-05 ++++ 0.0723453 1.0000000 chr5 158635248 RNF145 TSS1500
156000 cg10485752 0.1432 0.0327 1.20e-05 ++++ 0.0723453 1.0000000 chr1 26021655 MAN1C1 Body
11224 cg00668103 0.1210 0.0277 1.22e-05 +++- 0.0723453 1.0000000 chr7 100084730 C7orf51 Body
37478 cg02339198 0.1076 0.0246 1.22e-05 ++++ 0.0723453 1.0000000 chr19 52693970 PPP2R1A Body
33262 cg02067580 -0.0638 0.0146 1.23e-05 +— 0.0723453 1.0000000 chr1 153606662 C1orf77;S100A13;C1orf77 5’UTR;TSS200;1stExon
280471 cg19891452 0.2885 0.0660 1.25e-05 ++++ 0.0725094 1.0000000 chr13 112978703
235393 cg16353272 0.0961 0.0221 1.35e-05 ++++ 0.0736778 1.0000000 chr16 2124240 TSC2;TSC2;TSC2 Body;Body;Body
114654 cg07510163 0.1519 0.0349 1.36e-05 ++++ 0.0736778 1.0000000 chr2 44547313 PREPL;PREPL;PREPL;PREPL;PREPL;PREPL;SLC3A1;PREPL 3’UTR;3’UTR;3’UTR;3’UTR;3’UTR;3’UTR;Body;3’UTR
32578 cg02026246 0.1296 0.0299 1.44e-05 ++++ 0.0736778 1.0000000 chr11 22687589 GAS2 TSS1500
370643 cg27155653 -0.1019 0.0235 1.44e-05 —- 0.0736778 1.0000000 chr1 183604774 ARPC5;RGL1 1stExon;TSS1500
64658 cg04111999 0.1023 0.0236 1.46e-05 ++++ 0.0736778 1.0000000 chr10 22615540 BMI1 Body
131033 cg08654960 -0.1495 0.0345 1.46e-05 —- 0.0736778 1.0000000 chr16 85319859
109701 cg07168204 0.1217 0.0281 1.46e-05 +++- 0.0736778 1.0000000 chr5 149864599
280816 cg19916330 0.1027 0.0237 1.47e-05 ++++ 0.0736778 1.0000000 chr14 68038877 PLEKHH1 Body
259615 cg18228116 0.3476 0.0803 1.49e-05 -+++ 0.0736778 1.0000000 chr10 133995345 JAKMIP3 3’UTR
98154 cg06421138 0.1083 0.0250 1.51e-05 ++++ 0.0736778 1.0000000 chr6 111750934 REV3L Body
238518 cg16573251 0.0700 0.0162 1.53e-05 ++++ 0.0736778 1.0000000 chr12 123381231 VPS37B TSS1500
339775 cg24748746 -0.2174 0.0503 1.53e-05 —- 0.0736778 1.0000000 chr7 155738916
291461 cg20805880 0.1014 0.0234 1.53e-05 ++++ 0.0736778 1.0000000 chr15 73367293 NEO1 Body
121453 cg07984508 0.0906 0.0210 1.56e-05 +++- 0.0736778 1.0000000 chr15 77426719 SGK269 Body
112621 cg07367760 0.1087 0.0252 1.56e-05 ++++ 0.0736778 1.0000000 chr16 2911707
147224 cg09845489 0.2497 0.0579 1.63e-05 ++++ 0.0749701 1.0000000 chr7 157667853 PTPRN2;PTPRN2;PTPRN2 Body;Body;Body
146726 cg09809672 -0.1376 0.0319 1.64e-05 —- 0.0749701 1.0000000 chr1 236557682 EDARADD;EDARADD;EDARADD TSS1500;5’UTR;1stExon
316511 cg22938135 0.0935 0.0217 1.65e-05 +++- 0.0749701 1.0000000 chr5 175841493 CLTB;CLTB Body;Body
100415 cg06581201 0.1743 0.0405 1.67e-05 ++++ 0.0749760 1.0000000 chr6 168534038
93087 cg06039392 0.1302 0.0303 1.70e-05 ++++ 0.0754702 1.0000000 chr4 187476953 MTNR1A TSS1500
343712 cg25052374 0.0771 0.0180 1.78e-05 ++++ 0.0777924 1.0000000 chr17 76991253 CANT1;CANT1;CANT1 Body;Body;Body
307323 cg22159421 -0.3143 0.0733 1.82e-05 —- 0.0777924 1.0000000 chr11 34460182 CAT TSS1500
190817 cg13208054 0.0753 0.0176 1.83e-05 ++++ 0.0777924 1.0000000 chr17 25936354 KSR1 Body
58507 cg03700279 0.1001 0.0234 1.86e-05 +++- 0.0777924 1.0000000 chr2 44576358 PREPL;PREPL;PREPL;PREPL;PREPL;PREPL;PREPL Body;Body;5’UTR;5’UTR;Body;Body;Body
156274 cg10502904 0.1460 0.0341 1.87e-05 ++++ 0.0777924 1.0000000 chr10 131565289 MGMT 3’UTR
301085 cg21613693 -0.1303 0.0304 1.88e-05 —- 0.0777924 1.0000000 chr17 73501181 CASKIN2;CASKIN2 Body;Body
227727 cg15754901 0.1049 0.0246 1.99e-05 +-++ 0.0816637 1.0000000 chr17 5402972 LOC728392 3’UTR
336897 cg24531494 0.1549 0.0365 2.15e-05 ++++ 0.0871965 1.0000000 chr4 121993049 C4orf31 5’UTR
69534 cg04426031 0.1100 0.0260 2.27e-05 ++++ 0.0905245 1.0000000 chr7 1799192
114218 cg07479711 0.1114 0.0263 2.28e-05 ++++ 0.0905245 1.0000000 chr5 1524940 LPCAT1 TSS1500
248409 cg17332762 0.0966 0.0228 2.31e-05 +++- 0.0906822 1.0000000 chr3 106967639 LOC344595;LOC344595 Body;Body
35145 cg02192228 0.1758 0.0416 2.38e-05 ++++ 0.0921815 1.0000000 chr3 8809536 OXTR Body
171628 cg11691429 0.1703 0.0403 2.39e-05 +++- 0.0921815 1.0000000 chr2 947634 SNTG2 Body
128672 cg08487455 0.1666 0.0395 2.46e-05 ++++ 0.0936517 1.0000000 chr16 76311050 CNTNAP4 TSS200
202290 cg13946520 0.2956 0.0701 2.48e-05 -+++ 0.0936585 1.0000000 chr2 87017689 CD8A;CD8A;CD8A;CD8A Body;Body;Body;Body

Top 100 GO terms

X ONTOLOGY TERM N DE P.DE FDR
GO:0016209 MF antioxidant activity 83 4 0.0003353 1
GO:0098869 BP cellular oxidant detoxification 97 4 0.0008096 1
GO:0004601 MF peroxidase activity 49 3 0.0009488 1
GO:1990748 BP cellular detoxification 107 4 0.0010205 1
GO:2000171 BP negative regulation of dendrite development 25 3 0.0010763 1
GO:0016684 MF oxidoreductase activity, acting on peroxide as acceptor 53 3 0.0012599 1
GO:0097237 BP cellular response to toxic substance 114 4 0.0016410 1
GO:0098754 BP detoxification 130 4 0.0016700 1
GO:0005794 CC Golgi apparatus 1477 17 0.0030512 1
GO:0099631 CC postsynaptic endocytic zone cytoplasmic component 2 1 0.0031425 1
GO:0005078 MF MAP-kinase scaffold activity 11 2 0.0036667 1
GO:0030728 BP ovulation 20 2 0.0043379 1
GO:0051232 BP meiotic spindle elongation 1 1 0.0047115 1
GO:0004990 MF oxytocin receptor activity 1 1 0.0049495 1
GO:0050774 BP negative regulation of dendrite morphogenesis 14 2 0.0052437 1
GO:0032225 BP regulation of synaptic transmission, dopaminergic 16 2 0.0053970 1
GO:0010335 BP response to non-ionic osmotic stress 1 1 0.0059936 1
GO:0071471 BP cellular response to non-ionic osmotic stress 1 1 0.0059936 1
GO:0061000 BP negative regulation of dendritic spine development 11 2 0.0060264 1
GO:0010288 BP response to lead ion 22 2 0.0067367 1
GO:0004666 MF prostaglandin-endoperoxide synthase activity 2 1 0.0073230 1
GO:0090362 BP positive regulation of platelet-derived growth factor production 2 1 0.0075212 1
GO:0050886 BP endocrine process 78 3 0.0076888 1
GO:0051704 BP multi-organism process 1013 11 0.0080764 1
GO:0097711 BP ciliary basal body-plasma membrane docking 91 3 0.0103511 1
GO:0001990 BP regulation of systemic arterial blood pressure by hormone 35 2 0.0105805 1
GO:0001992 BP regulation of systemic arterial blood pressure by vasopressin 4 1 0.0106572 1
GO:0035037 BP sperm entry 1 1 0.0108844 1
GO:0061795 BP Golgi lumen acidification 1 1 0.0108844 1
GO:1905526 BP regulation of Golgi lumen acidification 1 1 0.0108844 1
GO:1905528 BP positive regulation of Golgi lumen acidification 1 1 0.0108844 1
GO:1903537 BP meiotic cell cycle process involved in oocyte maturation 2 1 0.0112336 1
GO:1903538 BP regulation of meiotic cell cycle process involved in oocyte maturation 2 1 0.0112336 1
GO:0048545 BP response to steroid hormone 329 6 0.0116089 1
GO:0019953 BP sexual reproduction 791 9 0.0117434 1
GO:0050321 MF tau-protein kinase activity 22 2 0.0117656 1
GO:0031337 BP positive regulation of sulfur amino acid metabolic process 1 1 0.0119192 1
GO:0050668 BP positive regulation of homocysteine metabolic process 1 1 0.0119192 1
GO:0071284 BP cellular response to lead ion 3 1 0.0120588 1
GO:0045987 BP positive regulation of smooth muscle contraction 31 2 0.0121754 1
GO:1902626 BP assembly of large subunit precursor of preribosome 3 1 0.0122891 1
GO:0048609 BP multicellular organismal reproductive process 769 9 0.0124007 1
GO:0035936 BP testosterone secretion 2 1 0.0124744 1
GO:2000843 BP regulation of testosterone secretion 2 1 0.0124744 1
GO:2000845 BP positive regulation of testosterone secretion 2 1 0.0124744 1
GO:0004382 MF guanosine-diphosphatase activity 2 1 0.0132654 1
GO:0032504 BP multicellular organism reproduction 789 9 0.0133388 1
GO:0044703 BP multi-organism reproductive process 943 10 0.0136047 1
GO:0072299 BP negative regulation of metanephric glomerulus development 1 1 0.0140367 1
GO:0072302 BP negative regulation of metanephric glomerular mesangial cell proliferation 1 1 0.0140367 1
GO:0019098 BP reproductive behavior 30 2 0.0140944 1
GO:0050666 BP regulation of homocysteine metabolic process 2 1 0.0143875 1
GO:0004046 MF aminoacylase activity 5 1 0.0145101 1
GO:1904527 BP negative regulation of microtubule binding 2 1 0.0147022 1
GO:0043001 BP Golgi to plasma membrane protein transport 39 2 0.0147435 1
GO:0090360 BP platelet-derived growth factor production 3 1 0.0148222 1
GO:0090361 BP regulation of platelet-derived growth factor production 3 1 0.0148222 1
GO:0008446 MF GDP-mannose 4,6-dehydratase activity 1 1 0.0148750 1
GO:0047191 MF 1-alkylglycerophosphocholine O-acyltransferase activity 1 1 0.0152431 1
GO:2001246 BP negative regulation of phosphatidylcholine biosynthetic process 1 1 0.0152431 1
GO:0003908 MF methylated-DNA-[protein]-cysteine S-methyltransferase activity 1 1 0.0152953 1
GO:0001963 BP synaptic transmission, dopaminergic 27 2 0.0157612 1
GO:0010193 BP response to ozone 4 1 0.0157812 1
GO:0004019 MF adenylosuccinate synthase activity 2 1 0.0158240 1
GO:1902816 BP regulation of protein localization to microtubule 5 1 0.0166441 1
GO:1902817 BP negative regulation of protein localization to microtubule 5 1 0.0166441 1
GO:0045907 BP positive regulation of vasoconstriction 33 2 0.0167987 1
GO:0033596 CC TSC1-TSC2 complex 2 1 0.0169103 1
GO:0051754 BP meiotic sister chromatid cohesion, centromeric 4 1 0.0170654 1
GO:0001544 BP initiation of primordial ovarian follicle growth 2 1 0.0173561 1
GO:0014065 BP phosphatidylinositol 3-kinase signaling 152 4 0.0174938 1
GO:0047159 MF 1-alkenylglycerophosphocholine O-acyltransferase activity 2 1 0.0179564 1
GO:0050200 MF plasmalogen synthase activity 2 1 0.0179564 1
GO:0021935 BP cerebellar granule cell precursor tangential migration 2 1 0.0180708 1
GO:0008502 MF melatonin receptor activity 3 1 0.0182369 1
GO:0033365 BP protein localization to organelle 927 10 0.0183281 1
GO:0034059 BP response to anoxia 3 1 0.0183810 1
GO:0045764 BP positive regulation of cellular amino acid metabolic process 3 1 0.0185377 1
GO:0072301 BP regulation of metanephric glomerular mesangial cell proliferation 2 1 0.0188547 1
GO:0016206 MF catechol O-methyltransferase activity 2 1 0.0188997 1
GO:0102084 MF L-dopa O-methyltransferase activity 2 1 0.0188997 1
GO:0102938 MF orcinol O-methyltransferase activity 2 1 0.0188997 1
GO:1900169 BP regulation of glucocorticoid mediated signaling pathway 2 1 0.0189176 1
GO:0010701 BP positive regulation of norepinephrine secretion 4 1 0.0190142 1
GO:0042713 BP sperm ejaculation 5 1 0.0191454 1
GO:0047192 MF 1-alkylglycerophosphocholine O-acetyltransferase activity 3 1 0.0191847 1
GO:0005150 MF interleukin-1, type I receptor binding 2 1 0.0192514 1
GO:0023024 MF MHC class I protein complex binding 5 1 0.0193178 1
GO:0032227 BP negative regulation of synaptic transmission, dopaminergic 3 1 0.0193314 1
GO:0016036 BP cellular response to phosphate starvation 2 1 0.0193647 1
GO:0043262 MF adenosine-diphosphatase activity 2 1 0.0194854 1
GO:0031335 BP regulation of sulfur amino acid metabolic process 3 1 0.0195627 1
GO:0042351 BP ‘de novo’ GDP-L-fucose biosynthetic process 2 1 0.0195690 1
GO:0008585 BP female gonad development 96 3 0.0201038 1
GO:0031394 BP positive regulation of prostaglandin biosynthetic process 7 1 0.0202188 1
GO:0060359 BP response to ammonium ion 4 1 0.0202812 1
GO:1905424 BP regulation of Wnt-mediated midbrain dopaminergic neuron differentiation 2 1 0.0203327 1
GO:1905426 BP positive regulation of Wnt-mediated midbrain dopaminergic neuron differentiation 2 1 0.0203327 1
GO:0044208 BP ‘de novo’ AMP biosynthetic process 3 1 0.0203449 1
GO:0003044 BP regulation of systemic arterial blood pressure mediated by a chemical signal 45 2 0.0203784 1